Actually, maybe something was overlooked. Reading through the documentation of XCCMC, to quote:

"mix - If your Mod needs to use files in other MIXs then ecache##.mix or expand##.mix, insert those MIXs here. Those MIXs will be inserted into expand##.mix."

If files are placed on an Expand##, YR 1.001 wont read them. I guess this could have been done to mantain support for RA2, just as Matze did with FA2 about 59-64 script actions, for example. Now i wonder if theres a special version of XCCMC that would output as Expandmds instead.