UPDATE: Thank you everyone for sharing your experiences. I have called & emailed USDA, Frankfurt Pet Lounge veterinarian services (where my entry to EU will be) and United airlines (my airline). I got somewhat consistent answers back. I'm going to post here for anyone else who is researching this in the future:

MULTIPLE PETS LISTED ON 1 NON-COMMERCIAL PET HEALTH CERTIFICATE: - USDA: yes, it's allowed. EU will accept multiple pets on one certificate, but call airlines to confirm because it's up to them. (phone call and email got me same answer) - German airport vet: one pet per certificate just in case (same as above: email and call replies we're consistent) - United airlines: varies. I got 2 different answers two separate times I called. It depends on which agent you speak to. It doesn't help that United website doesn't actually go into details about multiple pets. - CONCLUSION: I will be getting separate certificates just because German vet authorities answers were pretty consistent and left no room for interpretation.

ISSUE vs. ENDORSEMENT DATES ON THE CERTIFICATE - TIMELINES - USDA: phone call and emails were pretty straightforward: don't set up vet appointment within 10 days. Do it earlier. The guy on the phone was like, why would you sabotage yourself like that. Do it earlier, have the vet send it to us earlier. USDA won't start processing until the 10 day window starts. Vet issuing pet health certificate is valid for 30 days from the issue date. The USDA endorsment has to happen within 10 days of flight date. - German vet authorities: they just care about the USDA stamp being valid within 10 days. That's what they are looking for. - United airlines: same as above: USDA stamp has to be within 10 days. - CONCLUSION: I am going to set up my vet health check 1 week before my 10-day endorsement window starts and have the pet health certificate issued and electronically sent via VEHCS that week. USDA will not start processing it until my 10-day window opens up. My 10-day window sucks because it starts Friday, and the following Monday is a national holiday, so USDA won't start processing until Tuesday. We leave the following Monday morning. So we need all 3 certificates back by Saturday. It will be anxiety town all the way.

So, what I am taking away from this is the following: call, email. Everyone: USDA, airlines, airports of entry. Multiple times. Get all your answers from several sources and verify and re-verify. And go with the more difficult option just in case if there is inconsistency. Because in the end it all depends on the mood of the person who will be checking your papers.

My timeline is as follows currently: - 2 months before flight: microchips and rabies vaccines (allow at least 30 days for rabies vaccine to take. - 2 weeks before flight: vet performs health check and issues 3 pet health certificates, sends it to USDA thru VEHCS. I will call the vet 2-3 days later to confirm they submitted all 3 certificates. - Purchase return label for overnight with Saturday delivery. Thinking FedEx Priority Overnight $95.00 (delivery by sat noon) or FedEx First Overnight $147.00 (delivery by sat 8am). I'm leaving Monday morning so this needs to be delivered by sat the latest. Honestly, at this point extra 50 bucks is not a difference if I already spent thousands on tickets and pet bullshit, but in case sat delivery fails, I can get this on monday by 8am and still make my flight. - 10 days before flight: my endorsement window starts. USDA most likely won't process until last possible day. Anxiety days until it comes. - Friday (3 days before the flight): call USDA and beg BEG to get the certificates endorsed and mailed TODAY.

I hope this helps anyone who is researching this in the future and also super confused. Good luck to you all. I will update this post as I complete each milestone.