The issue isn't the existence of main::isa: You can do '$main::isa = \&UNIVERSAL::isa;' to create main::isa, and then call main->isa('Foo') and you get false as you should.

The problem is that the 'isa' installed by Test::Deep is 'broken' with respect to 'main': It causes main->isa('Foo') to return true when it shouldn't.