The CofG ALT option is just that, an option in the performance software. It nets usually one or two degrees higher ATM, but thats about it. All in all a minor performance impact. Some pilots did choose to calculate a bit more conservative and do not select that option, therefore keeping a slightly higher margin on the runway for the no-go case.
We do use two centralized load control centers in eastern europe that do all our load and trim sheets. They try to give loading instructions that lead to a CG that is as much aft as possible while still being operational viable, for example transfer bagagge needs to be in a different hold than local one so that through checked baggage can be processed faster to allow short hub and spoke connections.
The cruise CG thing is a totally different thing. We used to have absolutely no guidance about it at all, so every pilot did whatever he thought best. That changed when some captain as PM grew bored on a flight and decided to play with the FMC. Eventually he set the cruise CG to 36% which resulted in stall warning activation and an altitude loss of about 5000ft in the stall recovery procedure, of course without any notice to ATC in the moment.
After that we got a procedure to set the cruise CG every hour, based on our take off CG and the initial fuel load and remaining fuel at the time of recalculation. Eventually that was ditched for just leaving the pre-set cruise CG in the FMC and not messing with it at all. The pre set one is 8% CG and extremely conservative.