It could be. I really think we should make that error more explicit. In the case you describe, you would get the following message:
The settings for this document do not match the instrument type Thermo Altis:
Collision Energy: None
Would you like to use the defaults instead?
But what "defaults" exactly? Reading the code, it ends up taking the first settings in your list that start with "Thermo", which for a default installation is "Thermo Quantiva". So, that would work for you, and may have been what you were experiencing when you felt that accepting this message gave you values that worked on the Altis.
However, if you somehow ended up with a different list ordering where something else beginning with "Thermo" came before "Thermo Quantiva" then that could be a problem. I think we should be providing the name of the "defaults" Skyline will use to make that clearer.
Of course, your best option is to set what you want explicitly in Transition Settings and not accept the "defaults" which could vary from installation to installation of Skyline.