As Ovibos said, the SE line is a lower cost version of the Core line. The S2 line fits between. If it doesn't say "SE" or "S2", it is a core line model - with possible upgrades beyond that (see below). So the SE Standards are the lowest cost, the regular SEs next, then S2, then Core.
I have never heard of a "Custom Pro" PRS.
There are grades of guitar above the normal Core called Artist Package, Wood Library, and Private Stock.
"SE", perhaps apocryphally, was said to stand for "Student Edition" to denote the still-high-quality yet lower-cost model line, but that terminology was never officially used by PRS as far as I have found.