The rules on physician NIW are pretty well solidified and the recent lawsuit that was won serves to define them even better. If you provide 5 yrs of service in a HPSA/MUA then you are eligible for green card as per the legislation set forth by congress, much of the legal proceedings focussed on congressional intent.
The USCIS pretty much expects foreign physicians to use this method to migrate to the US. Of course they do not preclude us from the general LC based immigration but by creating this route their intent is that we follow it.
In the past LC based green cards were going through faster and with less stringent requirements and could be initiated during waivers hence people took advantage of it, since seldom do physicians nowadays have the courage nor financial risk taking ability to set up shop right away, most of us nowadays get employed to start off with, this was not however the way it was in the past.
Clearly the above said, if you were to move to a fellowship a pending NIW based petition is the safer way to do it. However, the problem is a little different. The law is the law, but a pesky USCIS officer can make a bad reading of the law and put you through hell requiring all sorts of legal challenges and so on. I doubt it will happen, but until you get the green card in hand, it is always a small risk if you move to a felowship.
I have decided that personally when I complete my commitment, if I suspect I will get the green card in 1 yr or less, I might stick it out, otherwise I will take the small risk involved.