Since the OP's sub l is within the same BEGIN block as use bytes this isn't really the issue (although placing the use bytes alone in the begin block causes the pragma to be scoped only to the BEGIN block. I remembered seeing an example of this type of thing in the source of RPC::XML. I'm guessing there's no simple way around the problem but here's one option (which you might have already discovered based on your original post):

package Y;
$VERSION = 0.1;
1;

package X;

my $subs =<<__SUBS__
sub l{ return length shift };
__SUBS__

if ( $Y::VERSION < 1 ){
    use bytes;
    eval $subs;
} else {
    eval $subs;
}
                                                                      
+                                                                     
+                
# large module follows
                                                                      
+                                                                     
+                
1;
package main;
no bytes;
$x = chr(3456);
print X::l($x);
[download]

BTW, use MODULE is the different than use PRAGMA. You can't use BEGIN { require PRAGMA import PRAGMA LIST; } when you're dealing with pragmas. The BEGIN {} creates a lexical scope of it's own and defeats the purpose of pragmas that affect the lexical scope. Plus, you wouldn't ever be able to do an import on the pragma.

Update: Solutions suggested below using the if module are much more reasonable than what I posted... Oh well :-)