I find it surprising that adding the modifier back later has no effect, and triggers no warnings. I guess I’ll just have to remember that once a regex has been compiled with qr//, its d, i, m, s, and x settings are thereafter immutable.

Well, isn't that the point of having a compiled regexp? Now, if you compile a regexp, you know exactly what you have. Otherwise, if I have a compiled regexp, I still don't know what it does, because modifiers can be applied. It also means that if you would do something like:

my $pat = gimme_pat();   # Some method returning a qr
if ($str =~ /^ $pat $ # Anchor pattern/x) {
    ...
}
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will break if $pat uses spaces.