If you log both lab caches and regular caches on a milestone day, there is a risk that milestones on Project-GC will be off since we don't get all the information we need from the API that we need.
You can't (as of now) manually change milestones on Project-GC, but as you say you can add a bookmark list that displays your milestones as you want them (but this won't remove the normal milestone display).