Is it OK to have Perl 5.20+ with $Config{randfunc} returning drand48 without the Perl_ prefix?

Yes, the user can always opt out of using perl_drand48, either on purpose or by mistake ... it is a weird thing to change

Also, the user can always fake/fudge Config.pm

simplest best option is trust Config

Is there some other method besides using %Config to check that Perl uses its own drand48 function?

see if any drand48 is imported with  objdump -x perl...dll |grep drand48

Or heuristics ... hahah :D