I've bought small quantities of PEMs (studs and nuts) from eBay in the past. Installed them with simple, shop-made tooling using a bench-vice. Works for me with small inserts (#4, #6 UNC). Commercial tools may make a stronger installation but mine were not highly stressed and things hold themselves together anyway after assembly.
Using simple tooling, you may not get them absolutely flush – a few thou proud (although I've seen that with commercial installation too). If that's important to you …. for example, in one case I installed PEM-Studs through the front panel of an electronic enclosure which would afterwards be covered with a thin overlay …. you can try using an end-mill to put a small (5-10 thou) counterbore on the hole before installation. Rub a bit of filler in if you're painting. Or skip the counterbore and just sand of the proud part.
PEMs can be a bit fiddly without proper tooling. It's do-able but you wouldn't want to bother unnecessarily. In certain cases though, they're a lifesaver and well worth the effort.