You are simply just going to be paying your accountant to file 3 tax files for 1 property. 

They also seem to be keeping up with the LLC state filings every year (I check the secretary of state website from time to time).

I e filed claims with both VRBO and AirBNB and had no issues having them paid.

You are subject to failure to file and failure to pay penalties.

It just seems like there will be many that fail to file their report and I just can't see the government really going after tiny businesses for so much money for something that is so easy to forget to do.

If I invest a multifamily through a Roth IRA, will I still receive the same tax benefits as I would with personal cash when I file my tax return?

It's typical and recommended one tax professional handles the entire filing.

Same goes for number of LLCs and what to fund them with, since bear in mind that CA tends to be more cumbersome and expensive to have LLCs than other states.California is generally more cumbersome than other states when it comes to taxes and filings.

I use Proper, but have not had to file a claim yet. 

Much like there's "organic" produce and "certified organic."