Let's see if I can clarify some things.
REAPER is simply better-tailored for Rock Band, EoF isn't.
Incorrect. REAPER predates RBN and is a full featured DAW. What we use of it for RB3 customs and RBN content is a small portion of what REAPER can do. REAPER was never created or tailored to RBN use. Instead, HMX realized it needed a good DAW with MIDI capabilities, picked REAPER for reasons only they know, and then set off to create the tools that would create the song files (Magma and MagmaCompiler).
So the point here is that Magma was created to expect and handle REAPER MIDI files created using HMX's template and instructions. RB3 can and will work with zero length notes, with MIDI files using running status, etc. Magma will not accept those files. Why? Because that's not what Harmonix wanted when they designed the system and they enforce those rules arbitrarily. As an example - Magma produced 256x256 DXT1 (lowest quality) image files for album art. But now Magma: C3 can produce up to 2048x2048 DXT5 (highest quality) image files for album art and guess what? They work fine in game.
Magma is the gatekeeper here, but only because of arbitrary restrictions that HMX put into place. A lot of those I removed and/or softened, but some of them can't be modified and you have to live with them. As a result, REAPER is the desirable place to work from.
I'm sure you can put together a Magma compliant MIDI using EOF or hell, using a binary editor. But using REAPER is ultimately the easiest way to consistently get Magma approved MIDI files.
EOF was created for charting songs for FOF...or did you all miss the "On Fire" part of the name? Naturally, since then, raynebc has improved and expanded into RockSmith, Rock Band, etc. Raynebc is an incredibly talented guy, but he is just one guy. He can't be expected to accomplish what the entire team at Cockos has been doing for well over a decade with REAPER.
So don't think of it as attacking one or praising the other. They both have great features, and they both excel at some things that the other does not. Unfortunately, some of the things that still need work on EOF can and does affect a MIDI's ability to pass through Magma and/or may create problems in game. So we recommend REAPER as that is what the designer of the game intended to be used. If you go outside what HMX recommended and the tools and tutorials HMX provided for the creation of this content - it doesn't mean you're doing something wrong...but you have to be open to the idea that you will break something and/or encounter difficulties solely as a result of your choice to go beyond what was intended.
So use EOF if you want. But don't complain when Magma refuses to compile your song, or if your tempo map isn't accurate, or if you crash your console.
If you manage to create a MIDI file that passes Magma and plays as expected in game, all using EOF - nobody is going to tell you that your custom is not wanted simply because you used EOF. Of course not.