So what is the penalty for missing the 90 day report?

You should contact the Embasy/consulate you intend to apply at to determine their exact requirements. They all have different rules.

I've had the same experience in Jomtien, must wait until the last 5 days to request a 30 day extension.

Also my understanding is if you enter the country with an O-A visa, they stamp you in for a year and you must report every 90 days.

It's not an issue when you check into a hotel as the hotels file TM.30s electronically for every guest. The TM.30 is only an issue if you own the property. You have to report every foreigner staying at your property within 24 hours. It's the owner's or manager's responsibility to file the TM.30 any they're responsible for the fines for failing to do so. So if you own your place of residence or allow a foreigner to stay at your place of residence (whether you own it or not) then you're responsible for filing the TM.30 within 24 hours.

Different countries have different rules. You need to check with the consolate/Embasy you'll be applying for the visa at for their requirements.

The non-O I was referring to was based on retirement.

I know someone with a non-O and a WP, but they were issued quite a while ago and the rules have since changed.

So what's the next step to transfer the visa to the new passport, or is that not required? Can you get another extension of stay in this case? Issues with 90 day reporting?

Sorry, no, missed the part about Singapore.