...I wasn't aware of needing to extend the rear bump stops if going with 4" of lift in the back. So much stuff to learn.
I'm hoping someone here has added 3-4" in the rear and actually used a set of 5125's.
You may NOT need to extend the rear bump stops, is all depends on the design of the lift kit.
There are several limits of the suspension travel;
Geometry: the links and suspension itself, it has to be stopped before the suspension pieces hit the frame with enough force to damage the parts. The links will only allow the suspension to extend so far, and there are many suspension designs where the suspension theoretically could extend is limited by when the links bind up or it sometimes needs to be artificially limited because other undesirable things can happen before the links bind up.
Spring/Shocks: The spring shocks have limits to how far they can extend and compress, it has to fit within the travel of the suspension otherwise you have mismatch and damage can result.
Driveshafts: Driveshafts have limits on the angles they go, especially with power going through them. Exceed the angle, the drive shaft may snap, or it may wear excessively fast. As well, driveshafts have an idle angle that they should spend most of their time transmitting power, outside that ideal angle, like if you've done a cheap lift to far, the driveshafts spends a majority of its time transmitting power, it will wear much faster.
Links and alignment: You've also got steering links, sway bar links and brake hoses that might NOT have the same extension as the lift, alignment might be different and angles can be different creating more stress. If you increase suspension travel, some suspension designs may create such a change in wheel alignment at those extremes its dangerous (the artificial limits I spoke of above).
Bottoming Out the suspension fully compresses with the whole weight of the vehicle behind it, that is a tremendous amount of force and that is why there are huge rubber blocks with a very strong part of the suspension hitting it to absorb that impact and prevent damage.
Hitting Extension limit just the weight of the wheel and suspension behind it, the forces are much less, and thus if there is even a bump stop, its small, in some designs the spring or shock is designed to absorb the force and be the limiter that keeps the suspension from extending farther than it should and damage the other things above. Don't take that to believe that opposite is true, that shock and spring can absorb the much more severe bottoming out force, that is where people end up with blown shocks and damaged springs. On some designs, like the Commanders IFS, the big sturdy Strut, has a huge sturdy rubber bump stop for bottoming out. If a suspension's original design doesn't have a shock strong enough don't think it will ever be strong enough to handle bottoming out.
In the debate over the front shock of the Commander, is it a strut or a shock? You can spend hours in an academic debate, the Commander has a Double Wishbone front suspension NOT a Macpherson Strut suspension. But, the packaging, production efficiency and performance of the Macpherson strut is so advantageous, they have gone to using modified Macpherson Struts in other suspensions even though technically they are NOT performing as a structural suspension link. So they call it strut, even if its just performing as the shock/spring/bump stop and rubber mount all in a convenient condense package that performs better, its the same part, just used differently.
So, you're going to lift you vehicle and change all this
A good lift kit has figured this all out and given you everything you need. But there are lots of bad lift kits out there, that haven't figured everything and given you everything you need.
If the lift kit leaves the suspension still able to compress all the way to its original compression to the original bump stop and the springs don't bind, then no you don't need new bump stops. The lift kit may very well result in binding or other pieces hitting and damaging before reaching full compression, which means the bump stops have to be modified. A good kit will include the modified bump stop, a bad kit will NOT and you'll likely damage your suspension.
Just raising the ride height, either with pucks/blocks or taller springs, nothing else, really doesn't get you much. There will be no additional wheel travel. The suspension will have the wheels extend to the same point as stock, which is less distance now, because you raised the vehicle by extending the suspension and taking away some of that distance for how far the suspension its limit in extension. You may have more distance for the suspension to compress, provided the pucks/blocks or taller spring doesn't cause the spring to bind before hitting the bump stop. If it does, there should be modified bump stops, so the end result, you've traded some jounce for rebound, and if you had to modified the bump stops, you've actually reduced the full wheel travel. There is some benefit in more ground clearance, thus more break over angle, fitting larger tires, but overall off road ability doesn't improve much without more wheel travel or decreased if you decrease the total suspension travel.
Live axles its easier to compensate for all the stuff I mentioned above, so the rear, you could use taller springs that don't bind with longer shocks (cause they limit the extension of the axle) and actually get more suspension travel.
The front on the Commander is Independent Front Suspension (IFS), this is NOT so easy to modify and the links in the suspension limit its total travel greatly, and driving around at a different ride height is more stressful on the steering and driveshafts, proportional to how high you lift it.
The severity of the lift is a factor, lifting it only 2", will likely NOT put all the Geometry to far out, to the point undesirable things will happen, perhaps wear might be a little accelerated, i.e. you might have to replace some suspension pieces a little sooner than if you kept it stock, nothing crazy. Judging from the posts on the forum, well in the range that arguably that parts that need replaced wasn't outside of the realm of the stock suspension.
A 4" lift? The kits I've seen are pretty radical, and that makes sense to me, there are modified steering knuckles for the IFS to compensate on the angles for steering and driveshafts. Perhaps that give you a little more wheel travel in the front. Shocks for the rear to produce the wheel travel, etc.