I actually had a similar experience with a friend. As mentioned, I did 2 years at BYU (pre-mission), then switched over to the Air Force Academy afterwards.

One of my good friends got a 3.6 his first year at USAFA, which is very good there, probably top 10%, at a school with higher incoming academic standards (by the numbers) than BYU. He then went on a mission and transferred to BYU.

He was barely able to be accepted due to his 'terrible' grades, and certainly couldn't compete for any sort of additional scholarship.

He then immediately got a 4.0 his first year at BYU. Given the courseload difference (18+ credits is the norm at USAFA), that only raised his GPA to about a 3.75, so he was literally laughed at when he went to apply for scholarships and told he wouldn't even be eligible with anything below a 3.8 cum. He then had another year of 4.0 grades, raising his cumulative GPA to just over 3.8 and went back to the scholarship office where he was told that while he was now technically eligible, his grades were so low that it'd be a waste of his time to apply. He did apply and ended up getting a scholarship for the last year of his education there so someone higher up clearly understood the difference, but it was definitely something where he struggled coming from USAFA to BYU.

Not because the courses were harder, but because the grade inflation at BYU was so much more pronounced that his good performance at a school with different metrics nearly prevented him from being accepted and then weighed down his grades for years afterwards. I'd guess something similar occurred with the one trying to come from Stanford.