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I have (temporarily) two CC tubas. They have slightly different intonation tendencies. Since they're both 4/4 rotary tubas, they feel similar enough that my brain doesn't think, "this is a very different instrument," when I pick one up.

So, I'd been playing one for a while. When I sent it to the shop for a repair and switched to the other, it had intonation issues, stuff I didn't remember bothering me before. After a couple of practice sessions, it was sounding pretty good. When I got the first horn back today, I picked it up and it now had tuning issues. I tried alternate fingerings I hadn't been needing, spent some time playing along with some drone pitches, and then, after about an hour, it seems fine.

Is this normal? I'm hopeful that I'm unconsciously playing the instrument differently, after a little time, so that it sounds in tune, rather than the alternative, which is that I'm hearing bad pitches and thinking they're fine. The tuner suggests it's more the former. Still, I was surprised at how much I noticed the switch from one tuba to another.

It also makes me wonder when somebody says he or she tried a tuba out briefly and it had either good or bad intonation, maybe it's more that the intonation matched or didn't match what they are accustomed to.

Your observations make perfect sense to me, as I have experienced the same.
And it´s not only Intonation, the way a horn accepts airflow is involved, too.

So yes, I believe we DO internalize our reactions to Intonation quirks, very much so.
And that´s a good Thing, too: our measures to counter such quirks are stored in "muscle Memory" over time, so they won´t use up too much of mental capacity that should busy itself with creating Music.

To answer the question in the subject line:

“Lots”