Ok I got it! Well, I have to give big props to BlackRainZ who figured it out. I kind of had it, but I wasnt aware of the createxmlbinary thing, so when I made half my changes, it didn't affect anything because I didnt rebuild the data file. But basically I created a seperate race, and change the RaceClassification to the name of my race. Then add a prereq to the starting buildings (such as labor pit, lore shop, etc). Like so..
<Prereq>
<Type>Race</Type>
<Attribute>Fallen</Attribute>
</Prereq>
Then you have to rebuild the data.zip (the ever important step I was missing!)
Now, since in my race's raceconfig (and race file) the Raceclassification is set to my Race's name (rather than Fallen...all Empire's seem to default to Fallen for raceclassification), those initial starting buildings don't show for my race, but show up for all other Empire factions. All other buildings for this race will have tech prereqs (seeing as how they have a seperate tech tree).
I nearly fried my brain getting this to work, and I'm not even the one who eventually got it to work! Oh well, onto the modding...