They will likely cut off a hand if you miss a check-in, especially if you're in another country.
Check-ins are for 90 days in the country. If you leave, you are not in the country. The last I knew (things may have changed), you do check-in when you return..
I would not change your flights. You should be good to enter on visa exempt.
If/when your DTV is granted, you will need to exit/re-enter Thailand to activate the DTV.
If you have no travel plans you can go through an agent to a near land border, cross, come right back (border bounce). You can do it yourself also, if you're into adventures.
I think you will be fine. If they pull you aside to ask more questions, play it cool. Explain how much you love Thailand (as you did in this post), explain your employment/life doesn't allow you to live their full time, but you enjoy spending your free time in Thailand. The immigration officers like hearing good things about their country.
I think people run into problems for one of two reasons, A) They're assholes who think they are entitled so they become combative, or B) they have a problematic history (black listed, then arrested, then ....).
You seem like a decent bloke who spends money in Thailand, you're exactly the kind of people they want in their country.
If you wait until the last day, you run the risk of not having all the necessary paper-work, then getting denied.
Usually you can a extension 14 days ahead of time. Each immigration office is a bit different on the 14 days, so really it's a matter of which immigration office you use. I believe BKK is 14 days.
I don't think it matters too much. In both cases, when you stamp in, you get 60+30, then you will have to exit and return. The METV saves you the hassle of re-applying every 90 days, but it's not necessary to get a visa (depending on your nationality). Hence, you're just throwing-away money but getting the METV.