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Since you were asking me before: I use TSRW, with that you can add as many colour variants as you want (which will actually be in the same object). The order in which they show up (to answer your other question) is determined by a flag in the COBJ labeled UnkCommon06 in s4pe, see here for more info:
http://modthesims.info/showthread.php?t=551120 . I don't think that's accessible from within TSRW, but not sure. You only need to fiddle with that when you want your colour variants to show in a particular order, by default they will all have a value of 0xFFFF in that field (I think I've seen 0x0000 too; 0xFFFF is what Maxis objects usually have).
I believe the underlying issue with "new swatches being incompatible with the recolour tool" is that when you stick different MODLs into the same thumbnail (I believe that's what S4S users often do to create more colour options) they are still different MODLs .. switching between the colour variants of *different* objects by way of the in-game design tool won't work, not with Maxis objects either, so even if/when they finally get around to fixing the limitation for 64bit instances those will probably still not work.
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