The difference is simply one is s visa that you pay for, the other is not any visa. But is a visa exempt entry stamp granting you the same 60 days the actual visa does. Over multiple entries, I think the visa exempt stamp gets scrutinised more than an actual visa entry.
and that being said, I left Thailand after 90 days and returned to the same address and didn't do a tm30 online based on what i read on various fb posts. That little episode cost 1600฿ in a fine 🤷♂️
I think the tm30 online is ok, until you need to show a tm30 to immigration. But as long as it is on their system, they just write a slip and fix that slip into your passport for free
I'd be saying your issue might've been that you had no visa at all. Though I did the same, came here with no visa, and at the end of 90 days, I went to Vietnam for 4 days and returned without a visa. Luckily I didn't have any issues.
If you're only intending to stay upto 90 days, no need to pay for a visa. Enter on visa exempt, get 60 days. If you need more, extend for an additional 30 days