Do I cause problems putting the grounding rods beneath the cement foundation of the cabin? The advantage is that I am not punching a hole through my wall which could lead to water issues down the road.
They might be difficult to inspect, but if the attachment to them is done with something that won't corrode or fall off, that shouldn't be an issue. So don't use a mechanical clamp, but instead braze or weld.
But it seems like a silly thing to do. OK, maybe you've avoided a hole in the wall, but what are you doing to do about all the other holes for feedlines, electrical service, water and waste lines, natural gas, AC compressor, etc?
If this is a new building, I'd build an Ufer ground. Most likely there will be rebar in the foundation: just take some care to make it all electrically interconnected, and leave some exposed at a few points for attachment. In some jurisdictions building codes require an Ufer ground as it's a reasonable way to get a ground with sufficiently low impedance in dry climates where a ground rod would be insufficient.
Should I bond the two grounding rods to the cabin ground system as well?
Most building codes require it. Not connecting the grounds can encourage static discharges which provide an ignition source. If the static doesn't ignite something, then lightning will when it arcs across the HVAC ducting, electrical wiring, and water piping since it provides a lower impedance path between the grounds than the soil between them.
If the fire hazard doesn't scare you, consider where you'd prefer lightning current to go: through a copper wire buried in the ground, or through your station equipment?
Does it matter that I will need to have the antennas grounded separately from my radio? The antennas will be at least 50 feet from my radio.
From an antenna performance perspective, no. From a safety perspective, no, as long as the grounds are bonded together as required by building codes. For lightning protection, you must have a single point ground, though if the antennas are also grounded in additional places on the unprotected side of the single-point ground (for example, at the tower base) that's fine, and often desirable to reduce the surge current. See How can I protect equipment against a lightning strike?
My AC/DC radio power supply connects to the AC ground. My radio's ground is connected to the power supply. Should I doubly ground the radio to the grounding plane and to the power supply? I guess technically I would be bonding to the power supply, but I am really trying to avoid RF issues.
If your feedlines are properly isolated from the antennas and free of common-mode currents, you don't need to worry much about your grounding situation (or lack thereof) causing RF issues. Best I can tell, the amateur radio grounding mythos is a holdover from the days when single-wire feeders were common. With a well designed antenna feed and proper application of baluns, grounding becomes irrelevant for RF performance since there's no RF current to ground.
Lightning protection is where it matters. Again see How can I protect equipment against a lightning strike? for more detail.