As long as the complete assembled rifle will fit in there leave it all together. That way you are faster to deploy. That is my take. I have two of the Starlight cases, best protection you can get!
I have one of the longer model 061352 (6" x 13" x 52") cut out for my bolt-action tactical rifle, it is reassuring to know that the scope will not get jarred no matter what.
My other Starlight case is the shorter "shotgun/tactical" size (model 061338) and my fully assembled 16" bull barrel AR15 with big scope that is used for varmint/target duty fits great in it.
Take your time cutting out the foam and it will look great and work superbly. To me it just makes good sense to put a valuable rifle in a top quality case, SPECIALLY if it has relatively fragile and/or expensive optics mounted.
enjoy!