it seemed that MPPT controllers are more efficient when converting higher volts/lower current into more amps to the battery compared to 12v.
The MPPT does a periodic check to find out what voltage gets the most watts out of the solar, and then operates the solar at that voltage until the next time it does the check.
So say you rig two 12v modules in parallel and the MPPT figures the Vmp right this minute is 17v. If you had it rigged in series, the Vmp would be 34v.
Either way the PV is operating at Vmp, so it doesn't matter which way you rig it, you still get the max watts the array can produce.
As for the buck conversion, it doesn't matter if you down convert from 17v 6a, or from 34v 3a...you still end up with 100w in from the solar and 100w out to the battery.
Wiring in series to raise the voltage and lower the amperage is very important when rigging a house for solar - it can save you a couple grand buying thinner copper wire.
But wiring a car with 5a of solar? Please, even with 10a of solar, you could use lamp cord and it would work just fine...and the "power lost due to inefficiency" would probably be measured in milliwatts.
As for a mis-match in Vmp of you two 50w modules vs. your 100w module, don't sweat it. The MPPT is just going to average out the whole array when it picks an optimal operating voltage.
It won't be the holy grail of perfect efficiency, but it'll be close enough.
And the truth is, with such a small system, you're not really going to see much benefit from the MPPT anyway.
So don't sweat it.