If I buy Morrowind on Steam, is the construction set compatible? If I make a mod, will it run with steam version as well as the other version? The only available version is the GOTY edition, are the bloodmoon and tribunal files separatable? So that I can make a mod that doesn't require bloodmoon and tribunal?

The Steam version doesn't come with the CS, but there are still ways to use the CS with Steam
And Yes, any mod with either CD or Steam versions will work for the other.

If you have GOTY, Yes you can make mods that do not require Tribunal or Bloodmoon. (just don't activate the esms when loading the CS)

Perfect! Thank you!