I'm glad you did this D&T. I hope they actually respond to this because it remains a head-scratcher. But, I'm not sure if they know the answer. Maybe they need the courts/congress to decide?
They don't need the courts or Congress to decide. There are no laws on virtual currency at the Federal level. The existing laws related to MSB are all here:
http://www.ecfr.gov/cgi-bin/text-idx?SID=4ed28aff321d97007276a7736cae032e&c=ecfr&tpl=/ecfrbrowse/Title31/31cfrv3_02.tplLook for section starting with 1010.
Section 1022 relates to MSB (and a MT is a type of MSB).
Section 1010 has definitions on various terms (including MSB & MT)
Section 1020 is rules for banks but some of those rules apply to MSB as well.
You will note the word "virtual" or "decentralized" don't appear anywhere in the actual law. What FinCEN provided in April was guidance. The simple version is that guidance is FinCEN way of saying "this is the way we interpret EXISTING law". No new law was created in April. Not a single line of public code. FinCEN has researched and reached the conclusion that EXISTING MT laws/regs apply equally to decentralized virtual currencies like Bitcoin. The pages of guidance are a way of forcing a square peg (virtual currency exchangers) into a round hole (money transmitters). However FinCEN didn't pass any new law and their guidance is just that guidance. If you disagree you certainly can ignore it (I wouldn't without legal counsel) and if/when FinCEN takes you to court they will layout a case according to that guidance. Now remember again guidance isn't law. Ultimately a judge however is either going to agree with FinCEN or they won't. If they do well you might be going to jail and if they don't then the guidance isn't worth the paper it was written on.
Sadly this process could have be avoided. Canada's regulator for example hasn't said they "don't" want to regulate virtual currencies like Bitcoin instead they looked at existing regs and rather than trying to do some legal gymnastics to make the existing law fit a new scenario declared "
nope the existing laws don't cover this". Now does this mean in Canada Bitcoin can not and forver shall not be regulated? Of course not.
It simply means the LEGISLATURE in Canada (aka the elected body who's duty it is to pass laws) will need to pass new laws if and when they want to regulate virtual currencies. Those laws won't need complicated legal gymnastics and pages of guidance because the laws will be written specifically for Bitcoin. The US Congress & FinCEN "could" have done the same thing. There are six categories of MSBs. Congress could have given FinCEN the authority to create new one "virtual currency dealer" or expanded the scope of "currency dealer" to include virtual currencies. Of course that process would be much slower, it would rely on the will of the people (though their elected officials).
The reason the guidance is nonsensical is because it is trying to apply regs written for one entity onto another entity. As an analogy imagine when the first passenger plane was built, there were no regs on passenger travel by aircraft. Of course there were regs on cars. The FTA at the time could have said. "well planes need regs and it is outside our Congressional authority so planes are cars. All regs on cars apply to planes". Of course that would create a lot of confusion given that for example planes don't (normally) travel on highways, have turn signals, etc. So the FTA could have provided pages and pages of guidance, creating from whole cloth entire new terms, definitions, and scenarios to try an fit a plane into the regulatory structure for cars. Thankfully they didn't. New regs were created dealing specifically with aviation.
TL/DR:
Guidance is FinCEN way of saying "this old law applies to this new stuff and here is how and why".
FinCEN doesn't pass laws so you are free to disagree.
One should expect to find themselves in court if your interpretation and FinCEN interpretation are not in alignment.
Depending on how strong your case is this could be a very good thing or a very bad thing.
Only legislature can pass new law and ultimately the courts will decide if the law is applicable.