Nope. Predefined units complete the prototype of all aspects of the unit whenever they are given. This is why in the original game, if you get Planetary Networks before you get Doctrine: Mobility, you can open a Probe Team in the design workshop, keep the Speeder chassis, and change everything else to whatever you're allowed to. At a minimum, you can design a Scout Rover this way.
My workaround / standard practice in my mod, is to only give a predefined unit 1 tech after the corresponding design elements were introduced. This is often not ideal because the time difference between Tiers of my tech tree can be huge. Like say, between Tier 4 when you get Doctrine: Initiative, and Tier 5 when you get Doctrine: Air Power. I've got a few Cruiser units available only with the latter, like the Cruiser Probe Team that has a radar on it.
It is also worth considering not giving a predefined unit at all, to avoid this problem. My general consideration is whether the AI would build a given unit anyways, or not. Predefined units can be a way of getting the AI to play better, if the unit is actually valuable as the AI uses it in practice. With a stock .exe, this takes a fair amount of playtesting iteration to find out, typically running AIs in play against each other. The AI, in practice, may not build a given predefined unit at all, regardless of how good an idea you thought it was. Or it may build it, but use it quite stupidly.
Generally the predefined units I've got in my mod, have received testing and have proven value to the AI. However, sometimes I realize that a predefined unit has adverse effects later on in the game, and I get rid of them one mod release later, after I realize that. For instance, I thought Scout Marines looked like a good idea for early game conflict, since in my mod nobody had any real weapons at the beginning. I thought, wouldn't it be cool if the AI starts attacking all these helpless Scout garrisons, with other Scouts, straight off of ships! Well first off, the AI liked to build the things but didn't really do that amphibious assault in practice. And second, it believed it was a worthwhile offensive unit later in the game, because of the "AI role" settings I had given it. It wasn't, it was just a waste of the AI's production points. So I scrapped it.
Plasma, 3-Pulse, and 3-Res armor are all related in that a prototype completion for 1, is a completion for them all. Similarly with Neutronium, 8-Pulse, and 8-Res armor. Similarly, Chaos and R-Laser weapons seem to be linked, at least when they have the same cost. I haven't checked on whether it's still true when the costs are changed. Tachyon and R-Bolt weapons are linked.
I have offered prototype units with 3-Pulse, 3-Res, one tech later than Plasma units, because I can presume that Plasma has already been prototyped by then. This may not be true if the tech was acquired through trade, but I don't personally care about that corner case.
One thing to remember, is you only have to worry about prototypes for chasses, weapons, and armor. You don't have to worry about prototypes for abilities. For example, there's no such thing as waiting to figure out how Trance works, it's instantly available when you research it. That's why I have so many Scout Whatever units. Nothing to prototype, they just encase a new ability in the cheapest way possible.
6 new categories and 72 new items added to the shop!
