Should work -- it just makes it confusing down the road later if you, a
future owner, or a service person ever needs to make changes or
troubleshoot something in the house, or if you ever do want to hook up a
second line. It won't be self-evident that the jacks wired as Y/B are
actually the primary incoming line.

Best answer is to hook up all four wires at each jack to their proper
terminals. Then, if you ever order a second phone line, you can then
just buy a two-line phone, plug it in and it will work on both lines.

Another solution (to avoid needing a two-line phone in the future) is to
replace each phone jack wall plate with a dual jack (i.e.
http://tinyurl.com/65w4x). One jack is wired with R/G wires to R/G
terminals, the other has Y/B wires to R/G terminals. Now you have two
phone jacks at each location -- one for each phone line. If you ever
order a second line, you simply plug any telephone into the second jack
to make the phone ring only on the second line.

Certainly you are *allowed* to do it pigtail both pairs of house wires
onto the same terminals in the "customer side" of the NID. The only
caveat is that it's non-standard and requires someone to remember the
house is wired that way to avoid confusion down the road. Unless you
have a *lot* of jacks on the secondary line, it really shouldn't take to
long to individually rewire them properly for the primary line or
replace them with two-line jacks.