The PSUs are all ATX compliant as far as power goes. Most of the miniITX motherboards have ATX-compliant power controls, as well (not all, mind you!).
There is no such thing as "miniITX power supply" as far as I know (barring the infamous PW200 POS). I'm curious to know what motherboard you're using that has a pinout that differs from ATX standard.
The 24-pin connector that you're specifying is the newest ATX standard. All the DC-DC PSUs sold in the mp3car.com store (as well as other vehicle PC resellers) that are ATX compliant do not provide the newer 24-pin ATX connector, but a 20-pin connector that works just fine with any ATX-compliant motherboard, even the miniITX boards you've looked at.
I think you're worrying over nothing, to be honest.