I don't get out here all the time but I drop by from time to time and thought I saw someone familiar here
What's the issue with the 5v VREF on the TPS? Does the Miata TPS not like that or something?
I'm sure we can do full standalone on these cars, keeping in mind these are ENGINE management systems so they're really not for everyone in the sense that a pure aftermarket EMS really isn't designed for the road at all due to EPA regulations and such. Using it for the road is really illegal then, but if you wanted to take it upon yourself to do so you'd need to either accept that this type of EMS functionality requires either a sacrifice of any non-EMS related functionality, or other ways to accomplish those goals, maybe by leaving the stock ECU around just for that particular feature you're looking for.
It's not to say the MS can't be made to do these things, but coding would be required to repurpose inputs and outputs. This will happen I'm sure but that's where it's at for the moment.
As for why your heater would need to talk to the EMS I can't really help you there
For the IAC you're right that it's just used for warmup at this time. I'd like to see that changed to support AC idle up or whatever other idle-up needs there may be (putting an auto in drive/reverse?), but that's back to further code development and allocation of I/O for these features. The MS3 will remove the I/O limitations but is a ways off still....