Their mods work with the Steam version.
My copy is a Steam version and I've tried TMO 1.9 and RFB 2.0 along with a few extra sub skins and DDEnvironments. They work as they should.
There is a catch with Steam use though. You MUST ensure that you have the vanilla 1.5 copy working first. You run the UBoat mission version. Steam will list both but you only want to run the UBoat add on version.
Once you get the vanilla game running. You go back to your games list in Steam and select properties for both games SH4 and UBoats and turn off the "Keep this game updated" to not update. Then you can put the mods on. If you do not turn off the updates, Steam will think SH4 got corrupted and start replacing the modded files back to the original. And it will do this while SH4 is running. Ask me how I know.
There are some problems you might not like with these mods... TMO makes planes too invulnerable for my liking. Also TMO's DD and DE destroyers accelerate like speed boats. A bit too unreal for me. DD and DE are SHIPs after all. They can't go from 0 to 37 knots in 5 seconds like it does in TMO. Looks great though. RFB 2.0 with newest patch has a serious bug that makes way too many DD destroyers. In the game, a lot of ships "just appear" (planes too) when the player triggers something. Like sinking ships in a harbor. RFB made about 90 too many destroyers out to get me. Causing the game to crash if I was on the surface approaching them (about 50nm out).
See the following picture screen shot...
The crashing was not because the video couldn't draw that many ships. But because the eagle eyed lookout watch couldn't handle the overload of reporting the great number of ships they suddenly see.
Anyway, my game would crash to desktop every time. I finally got past that "task force of DD Destroyers" by staying under until they passed out of the 50 nm range. Only to have the same problem again about 300 nm more miles away. I finally uninstalled the RFB mod.
BTW, I only had one mod installed at a time. TMO or RFB. Not both at once. I'm now going back to Vanilla and might add simple visual enhancements like new paint skins and environments.