Simply put, no, not if you want to get a run verified on the leaderboards. There are 3 emus listed in the rules. If PJ64 1.6 isn't working for you for whatever reason even after double checking the pj64 setup guide, try Rosalie's mupen. You can also join the discord for actual help with setting stuff up if need be.
the guy should probably update that link/mirror version to PJ64 Legacy 1.6 bcuz PJ64 1.6 has a vulnerability (which, even though you guys arent using rom hacks, I would use Legacy just to be safe)
You need a bad rom in order for that to even happen in the first place and the guide does list the checksums you can verify with. Even if thats the case, Rosalie's Mupen is the alternative if you don't wanna be super paranoid about it.
If you wish to replace your twitch highlights with reuploads, please edit your already verified run rather than deleting the verified run and making a new submission. This makes it a lot easier for us to track which submissions are reuploads and should be less work on your part as well.
If you need
