No. The Go 1 compatibility document doesn't say that anything about
the unsafe package can change. It says that packages that use unsafe
"may depend on internal properties of the Go implementation." That is
not intended to mean that such packages depend on internal properties
merely because they import unsafe. It is intended to mean that
packages that import unsafe may then (perhaps accidentally) use the
unsafe values in ways that depend on internal properties. The
atomic.Load/Store/SwapPointer functions don't use the unsafe values in
any way at all. They just move the values around. That is always
going to be OK.
Even if it somehow wasn't, the Go 1 compatibility guarantee does cover
the sync/atomic package. That package is guaranteed to remain
compatible, so atomic.Load/Store/SwapPointer will continue to work as
they do today, even if the unsafe package somehow, unimaginably,
changes so that they don't.