If you are going to install flex 99.5% of the way, why not run the flex those few final inches and go into the box with the swtich? The only thing I can see that would keep you from doing that is if the switch box is plastic. But if you can, I would run the flex all the way.
Now, there's two types of flex I envision you using. One is flex that already has the wires in it (commonly called BX, AC or MC). If you are going to use that, you will need a junction box to convert from the romex to your flex.
The other type, FMC, or flexible metal conduit, does not have any wires in it. You would technically not need a box to convert from one wiring method to another, but romex is not going to be easy to pull into it if you are going any considerable length. And the longer the run and more bends you have, the more difficult it will be to pull the NM in.
If I were given the above choices, I would prefer:
1: MC (with wires already installed) continuious between the two points.
2. MC to a j-box behind the switches if the MC cannot be connected to the switch box. A little more money and time, but insignificant compared to doing it wrong and have problems later.
3. FMC and struggle all day pulling the NM in.