The easy answer? Make it all up. Unfortunately, the ship system can be wonky, because not everything is set in stone, plus several ships don't even follow the design rules they layout, though I think those are in other books. I'll answer as best I can.
So I am thinking the price tag is basically for the barebones ships/stats. Then you add on systems based on the emplacement points available. Are these additions all considered standard modifications?
In my opinion, yes. The rules don't say, but since adding things can be considered non-standard then I would say if you are designing from scratch then yes, they are standard.
What is the limit to standard modifications for a starship designer when designing a new starship? Also, is there a point buy system associated with initial stats? IE can a Starship Designer move points around on the ship's stat line as long as it is equal to the starting stat value (like point buy character creation)? Also is there a way to "buy" better stats other than the equipment bonus thrusters, armor, and such?
To my knowledge, no. At least not officially, but if you feel they could as the GM, then sure let'em do it.
I get a kick out of equipment and ships and designing building them. This system, however, is off. I dunno if stuff got dropped form the book or a supplement was planned, or something, but it seems unfinished to me.