(1) Is it a good idea to nostart all provinces but those that are in ideal spots? (Probably about 60 or so provinces on the map, out of 605 or so.)
I'm a little rusty, but I suggest using #start. Just be sure to place enough #start locations to cover the number of players.
2.5.1 #start
By creating at least one start location for each
player, every player will start at one of these
locations. If #start provinces are set, nations will
start at these locations unless there are more
nations than #start provinces. If there are more
nations than #start provinces, the extra nations
will start in eligible random locations.
(2) Does SemiRandom ignore nostarted provinces?
It will ignore nostart for purposes of placing custom provinces, but it will not ignore them when placing starts (as of version 1.07). It is also worthy of noting that when it places a custom province it will mark that province as no start (unless it's intention was to place an actual start. 
)
(3) What is the best way to go about it for maximum flexibility? (So that the map can be used as is with or without the start provinces I specstarted.)
Include multiple ".map" files. (In my opinion. )
MyMap_WithSpecialStarts.map
MyMap_Plain.map
etc...