It gets down to the specific mod, your technical/mechanical ability/competence, tool supplies, and the complexity of the specific mod.
Face it, guys (and gals), the better dealerships spend a decent sum on training their mechanics and they know a HECK of a lot more about Toyotas/Scions than most of us do and also have been specifically trained for the vehicle and have the CORRECT tools for the job at hand.
Thus, it ALL depends on the mod, the tools required, and your competence and tools. CAN you do it correctly and accurately?
If so, go ahead.
If not, have the dealer do it, esp. if it is a TRD part . . .
--Most won't do a non-Toyota/Scion aftermarket part, unless you are lucky enough to have a Sparks-esque dealer nearby . . .