The CMS is about two inches higher than the Basis system (CMS height = MFT3 height, Basis height = old MFT height). You can attach the CMS to the MFT3, and the Basis to the old MFT.
The CMS uses different side profiles (same as the new MFT3, the Basis used the same side profiles as the old MFT). This means Basis accessories which use the top groove in the side profiles (such as the fence) won't fit the CMS. All these have new versions for the CMS, though.
The CMS also weighs a bit less than the Basis.
The Basis 1 insert (ATF55 saw) does not fit the CMS system, but all other modules will, and vice versa. Things like extension tables and slide tables made for one system will usually not fit the other system.
A thing to note is that the fence on the Basis can be tricky to position exactly square or parralel to the blade, as it is fastened with two knobs. If you tighten one more than the other, the thing skews. This has been improved on the CMS where a block is pulled into the V-groove, which automatically positions it straight and square. For ripping on the Basis, there is an special clamp available which holds the far end of the fence in place. I never rip without that.
I do not know what you mean by an old an a new CMS, as far as I know there is only one CMS.