In answer to question one, yes, you are correct, MAYBE. Let me explain:
If you use positional controls for two co-axial holes then you get a "bonus tolerance" IF you use the MMC symbol, otherwise RFS (regardless of feature size) is assumed (This is by the way a FUNDAMENTAL departure from the earlier 1982 version of the spec., which assumed MMC. That is why it is important to use the datum symbols specific to the version used on the drawing and specify on the drawing which version is to be referenced, otherwise the machinist may be unclear as to which basic rule is to be applied and may apply it incorrectly.). If the holes are larger than MMC, the difference between the actual size and the MMC is the bonus.
In answer to your second question the paralellism callout references the specific datum plane in question. Which is fine for flat planar surfaces, but a cylindrical surface datum makes deciding which of the two 90 degree planes to use difficult. Paralellism is never used for bores, at least not in my experience, it just doesn't control cylindrical surfaces well for the very reason you stated, at least not to each other. So to be honest the question is a moot one.