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Here's how:
1) Give the standard MCV to GDI only. Repeat: only GDI...
2) Clone standard MCV and give it to Nod. And i mean ONLY to Nod ;-)
3) Clone the standard MCV again and give it to the third side, and ONLY to the third side. MAKE IT DEPLOY INTO THE 3rd SIDE'S ConYard!!
4) Now proceed and set the tags AllowedToStartInMultiplayer=no <-!!
for ALL units EXCEPT the 3 MCVs.
5) Make sure the StartingUnits tag's value is set to 1 (it's at MultiplayerDefaults)
That's it

BUT
You cannot make a separate conyard for Nod. So, the new Nod MCV will deploy into the standard ConYard, but when you UNdeploy this conyard, it'll be a GDI mcv. So this will look a bit weird if your Nod MCV uses a different image than GDI's (like in TSTW)