Good question. If the settings you are interested in do 'ride with the file', then you should see them defined in an ASCII export. After a quick search of an ASC file I didn't find any instances of 'isol' so 'remove isolated copper', but it is defined in the PLANEFLAGS data.
PLANEFLAGS OUTLINE ALL Y Y Y N N Y Y N N N Y Y N Y Y N N N Plane and Test Points flags
You'll need to read Ppcb_ASCII.pdf for the decoder ring (i.e. that first Y means isolated pours are removed)
Drill oversize is defined:
DRLOVERSIZE 114300 Drill oversize for plated holes
So ti appears the two parameters you mentioned do run with the file. Hopefully someone from Mentor can give a definitive answer on this.