Bicycle Mechanics - Brand Spankin' New Park Tool PCS 9 Question

OK, I just bought my first work stand for my bike. Is it a major faux pas to use the clamp on the tube if I am careful not to crush the tube?

You can do it, just be careful. Many a frame have been ruined by being clamped wrong.

Don't clamp over a braze-on cable guide, if you forget and spin the frame it'll snap it or bend it.

Don't clamp over water bottle bosses with just bolts in them, can dent the tube.

Be careful with really light weight frames, even steel ones.

If it takes a round seatpost, clamp to that. If you have a carbon seatpost, pick up an alloy one to clamp to. If you have to raise the seat, do that too, they're a PITA if they seize, moving the post will also help avoid it seizing in the frame. If you're anal about your setup, and have to raise the post to get enough clamping area, a single wrap of [electrical] tape is a great guide for your seat height.

Go ahead, clamp to your thompson. depending, you might want to pick up a "rack" post anyway.

Steel and Ti frames can be clamped if you are careful where you place the clamp and don't cinch it down excessively. Aluminum and carbon frames should be clamped at the seatpost and the use of a sacrificial cheap seatpost of the proper diameter is a good idea.