I had a go today at installing hud mods with the FOMM Fork as run through the latest Mod Organizer, and it seems to have gone well.
I set up my "basic pack" of mods as a base (PN, iHud, Primary Needs, uHud, DarN for TTW, and a couple other gems like MCM, CASM, the Weapon Mod Menu) and installed them with the FOMM Fork as run through Mod Organizer, and then what this gives you in Mod Organizer is a little warning in the upper right corner and the Overwrite on the left panel goes red.
The advice given by MO is to drag and drop or make a mod of the files so that they may be moved onto the left panel with the other regularly installed mods and thereby interacted with, so basically I just made a mod by right clicking on the red Overwrite of all the files held within (the whole "basic pack" above), and then ticked its box to install it and all the esps and esms appeared in the rightpane of MO with all the rest.
At first glance, opening up menus in-game, playing around with iHud and things, it seems to have worked.