Interestingly it does flag the aliases for me:

$ perl -MGetopt::Long -we 'GetOptions ("a|x" => \$x, "A|y" => \$y);'
Name "main::y" used only once: possible typo at -e line 1.
Name "main::x" used only once: possible typo at -e line 1.
Duplicate specification "A|y" for option "a"
$ perl -MGetopt::Long -we 'GetOptions ("a|x" => \$x, "b|X" => \$y);'
Name "main::y" used only once: possible typo at -e line 1.
Name "main::x" used only once: possible typo at -e line 1.
Duplicate specification "b|X" for option "x"
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So if either the primary or the alias is non-unique in a case-insensitive way, the warning is shown. I'm using version 2.52 of Getopt::Long.

I'm also using Getopt::Long 2.52 (and perl 5.36.1). I also get the warning with your invocation. But my original code does not get a warning.

After adding debugging lines to Getopt/Long.pm, I see it's because use warnings does not set $^W (in contrast to the -w option that you used, which does). As in:

perl -M'Getopt::Long -e 'use warnings; my ($x,$y); GetOptions ("v" => 
+\$x, "V" => \$y);'
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Getopt::Long uses $^W to decide if the warnings should be reported ($dups is the built-up string of warnings, which is correctly set):

  if ( $dups && $^W ) {
        foreach ( split(/\n+/, $dups) ) {
            warn($_."\n");
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Judging from https://perldoc.perl.org/warnings#Reporting-Warnings-from-a-Module, I guess Getopt::Long should not (solely?) be looking at $^W nowadays?

Grepping the 5.36.1/ directory, I see some 30 other cases of "if.*\$\^W". So the end result is apparently that a few warnings in core modules are missed when using "use warnings", but shown when using -w ...

I think it likely that the majority of those 30-odd cases (including Getopt::Long) are bugs, though it isn't clear how they should be handled in a world of lexical warnings. Please could you raise an issue ("New issue" here) so that the perl porters can start to consider it for 5.40?