While I find the comments about core strength and related back health useful, simply looking at the core issue (sorry 
)… I think the question about what exactly is different between inside and outside is important.
This leads to my typical observation that most trainers inside lack any motion, while outside (especially on MTB) we are riding a very mobile and variable position bike. With a normal trainer setup, you are instantly locked into position that is not a replication of what we get outside. Added to that, there is a tendency to stay seated more vs standing for breaks or even terrain (again, regular MTB experience).
So, considering that and the potential for adding motion to the setup (via full rocker plate or even simple foam blocks) could be worth a look at the very least. I can help with more info, but will stop my rocker spam at this point 