Biowaste Blob's second ability doesn't trigger if you don't control a commander immediately as your upkeep begins. Players can't choose to take actions during your turn before your upkeep begins. If you don't control a commander when the trigger resolves, it won't create a token. These don't have to be the same commander at both times, however, and it doesn't have to be your commander.

Biowaste Blob's first ability affects itself.

The token copy won't copy counters or damage marked on Biowaste Blob, nor will it copy other effects that have changed Biowaste Blob's power, toughness, types, color, and so on. Normally, this means the token will simply be a Biowaste Blob, but if any copy effects have affected the original Biowaste Blob, the token will take those into account.

If Biowaste Blob leaves the battlefield before its triggered ability resolves, the token will still enter the battlefield as a copy of Biowaste Blob, using Biowaste Blob's copiable values from when it was last on the battlefield.

The token copy will have Biowaste Blob's abilities, including the ability to create token copies of itself.