RTF is a global modification that replaces all towns in the game.

Then we need different ones for the lizardmen.

Indeed... so let's create new ones.

Do you happen to know if it's possible to make mutually exclusive buildings in Heroes 5, like in Heroes 4 and 7?

I don't think so, but SRD came up with an interesting alternative:
we create two equally strong units and place them in an upgraded building, but they remain without the upgrade.