This is off the top of my head.

>Is there a terrain type which they cannot see me or fly to me
>within?

Generally speaking, if they can see an area, they can see you in any room in that area.

Some air forms have problems flying to indoors, but not all do. You can't fly into a guild, to underwater, or into a cabal HQ.

>Are there rooms which protect you from being flown up
>to/seen like being within a guild(can they even see me within
>a guild?).

They can see you within a guild (see above).

> Any way to determine this from within the room if
>you are not a shifter?

Generally speaking, the places you can't be seen from above are areas that are wholly underground. For example, the sewers or Underdark area of your choice.

>Is there a terrain type which when they
>fly into they cannot retreat from by "flying up"?

You can't fly up from a no-recall room.