I'll say up-front the advantage that the EEC series of computers have over aftermarket is that they're street legal, unless you modify their programming which basically makes that point moot.
The only MS boards that aren't surface mount are the roll-your-own v2.2 and v3.0 boards. Half of the intention with them is not just to save you money to build it yourself, it's an educational platform for you to learn about electronics, build circuits, and then get to actually do something with them.
All the other boards, the microsquirt, the v3.57, the daughter cards, all of them are manufactured boards with almost all surface mount reflow-soldered components. The EEC-IV is no different. Some components are surface mount, others are through-hole.
3.57 board - everything is surface mount except some transistors and some high wattage resistors.
EEC-IV - In addition to through-hole transistors there are through-hole resistors, diodes, and capacitors.
And what are you talking about fully potted? The EEC-IV is not a potted board. Neither is the EEC-V, here's a picture of one.
The EEC family of computers do die, and not all that rarely, which is why re-manufacturers like A1 Cardone bother to re-manufacture them (Example Part # 78-5611)
I understand that it might seem intuitive that the OEM computer must just be some better bombproof item, but that assumption does not stand up to scrutiny. I'm not saying it's any worse but I don't see any cause for it to be any better because it isn't different stuff, it's all the same stuff.
As far as the code goes since you bring it up again, that's your taste that you're welcome to hold but it isn't actually realized as a tangible impact. Regardless of your taste what matters is how the code performs, not how it is written. I got $20 that says you also haven't seen the proprietary code running Motec, Haltech, or Autronic which could be more or less suited to your coding taste, but if they work they work. Thousands of people use them and megasquirt successfully without any consideration for anybody's coding taste.
As an aside, while the MS code isn't exactly open-source (licensing is different) the source is openly-available and the whole point of openly-available source is that it has far more exposure for scrutiny and feedback. More often than not the globe can write better software together than a couple really smart engineers hunkered down. MS code has benefited from its exposure over the years.
The only situation where the code not being written to taste, or even well, is how it may inhibit bug fixing or feature enhancement however the megasquirt code is actively maintained and enhanced regularly by several developers around the world so this is a non-issue. A few individuals like GsLender and Whittlebeast have picked it up and did actually modify it to their needs and I never saw any of them complain that the code was too remedial so I don't see any risk of future support evaporating. There are plenty of people that are happy to jump in and work with it.
You don't have to rewire a plug and play which is the point of that product. You don't have to rewire a non-PNP version either, you just have to make the point-to-point wire connections from the new ECU to the factory ECU plug as an adapter harness or cut off the factory plug.. this is essentially the same thing as an aftermarket radio install with more wires. A full re-wire is of course an option but no more necessary than it is for an EEC.
A/C load, megasquirt handles that the same way the ECU does with closed-loop idle control but if you want you can also send the A/C on input to megasquirt and use it as a modifier to the idle control algorithm and/or timing control if you want to. Voltage compensation is all there too for injector drivers and coil saturation.
As far as miles going down the road, I'd have no problem sending a megasquirt 5,000 miles up the road. There are commercial businesses who manufacture flying drones and run them on megasquirt.
I looked at it 8 years ago and now that I've looked at it closely again things really haven't changed. The factory EEC is not less expensive, it's not easier to work with, it's not more capable, and examining the claim that it's more reliable turned up nothing.
Megasquirt can be less expensive, or more expensive, there's a lot of options here to fit whatever the budget, needs, and desire to "learn it" or "just run it" is. Megasquirt is absolutely easier to work with. Megasquirt is absolutely more capable. For reliability there might be some merit to this for an amateur build of a v2.2 or v3.0 board but not for anything else in the product line.. hell you can run an MS3-Pro underwater because it's completely water-tight.