I've done it. BUT it's tricky and takes lots of modifications.
First thing to remember is 1 SP is $10,000 C-Bills.
10 SP is 1 WP.
Basically you play the tracks in book as you want. But you need to convert back and forth between C-Bills,SP, and WP and use the GM mode and add an subtract funds from MekHQ.
With the currency conversions in place use MekHQ to repair, buy supplies, etc.
Use the non-AtB scenario abilities in MekHQ to build the scenarios (see the included scenarios as an example). Launch Megamek from MekHQ in the scenario.
Once in Megamek use the RATs or Force Builder tools to make an Opfor. Play and resolve back into MekHQ.
It's more work to juggle the tracks outside of MekHQ but very doable. I did find that some of the rewards converted to C-Bills where low but just tweak them to be fair.
When (no ETA) we get Story Arcs this will be the first book I convert for them.