Actually, when the AI builds vehicles, they will instantly spawn on any free cell directly next to the war factory, which can be on any side of the building.
The reason why the AI's war factories don't play an animation when a unit is produced and that the units instantly spawn instead of driving out of the door is related to the work-around that was necessary to allow the AI to build naval units (and prevent the AI from building these naval units from the war factory or tanks from the naval yard).
There is no other method available to do this, but considering it's either this or making the AI unable to build ships again, I'd say it's a very small sacrifice compared to the benefit.

Nukes can only be fired from a single structure in the game and because the Temple of Nod that the AI builds is actually a different structure that just looks the same (which is why it's not capturable), nukes can't be fired from it.
The nukes fired the Red Alert missile silo are actually a modified TS EM Pulse superweapon and the AI is simply unable to use this superweapon.
So in short; the AI isn't able to fire the nukes because of engine limitations which currently can't be circumvented.

This is related to a work-around to allow all factions to have different MCVs and Construction Yards, while still allowing the Short Game multipalyer option to work (the Short Game option makes all of a player's units instantly die when that player has lost all structures). Unfortunately the MCV is no longer recognized as the "Base Unit" by the game, so I had to do a work-around which basically delays Short Game for a short amount of time.
As a side-effect of this work-around you'll now also lose the game if you repack your Construction Yard into the MCV while having no other structures left or if you wait too long before deploying the MCV after the game has started. This can be avoided by simply disabling Short Game, but this means that you'll end up having to look far that last pesky (possibly cloaked) unit after having defeated a player.

Glad to hear that; I hope these issues won't get in the way of your enjoyment too much. Whenever a solution for any of these issues presents itself, it'll be implemented right away, but I can't say when that will happen.

I hope solutions will be found to.

There is another question I wanted to ask. Is there a possibility that yall would take out the Allies and Soviet additions to this mod and making a Red Alert mod for TS? Or have yall put this into consideration yet?

The RA factions have only just been added, so taking them out again would be silly. If you don't wanna play as an RA faction or against an RA faction, then pick a TD faction for yourself and the AI (or if you're playing online, ask the person you're playing with to select a TD faction).

I was just curious to whether or not yall were planning on doing another mod the focuses on RA. I do enjoy TD more than RA but I have no problems with the RA additions.

Why would we make another mod that focuses on RA when we've already added the RA factions to DTA?

It was just a thought.