Does anyone have any suggestions for how to get around these restrictions, or know which if any municipalities don't have these kind of restrictions?

I think if you were sharing walls or in same house, then certain quiet hours in lease or noise restrictions can help prevent some issues. 

My guy has access to batch skip tracing and lead stacking, call tools, and Propelio and I have Listsource preferred rates, Idi data, Rei Reply and Propstream.

Some lenders will require secondary appraisals, or a desktop appraisal, will want to see some sort of improvement on the property, and may have cash out restrictions. 

Here in St Augustine, they are banning certain neighborhoods, and putting restrictions on others.

If it's not a corner parcel and there's no access to an easement alley on the side or rear you will also require a breezeway on the ground level which narrows the ground level footprint and depending on the width of your parcel, can make the commercial space less marketable.

You can cash out after 6 months from date of acquisition, but only up to the limited LTV restriction of 50%.

I understand there are sq. foot restrictions based on the loan type.  

I’m aware California is not the best market, with the restrictions and potential new tax coming up, etc, but we have personal reasons to invest there.With that said, we visited a lot of houses in the San Diego area and saw 2 that seem like a potential fit for us: one is a smaller 3 bedroom but a mile from the beach and the other is a 15-17min drive to the beach, but bigger with 4 bedroom and a little cheaper, which would allow us some cushion to invest on a hot tub or potential pool.

Most people will not want to spend time on a deal or partnership if the numbers are too tight.Your other value here is:- You have full access to the property.