One thing that I heard from folks who do development for retro Atari platforms is that the 68k support in GCC has been getting worse as time has gone on, and it's very difficult to get the maintainers to accept patches to improve it, since 68k is not exactly widely used at this point.

Specifically, I heard that the 68k backend keeps getting worse, whilst the front-end keeps getting better. So choosing a GCC version is a case of examining the tradeoffs between getting better AST-level optimisations from a newer version, or more optimised assembly language output from an earlier version.

I imagine GCC 6.5 probably has a backend that makes better use of the 68k chip than the GCC 11.4 that ngdevkit uses (such as knowing when to use dbra) but is probably worse in other ways due to an older and less capable frontend.