How far you deviate from the manufacturers installation instructions should be a "common sense" approach (I know used those C S words again), but if the wire nuts are rated the same wire size, etc., etc., I don't see a problem. I sure wouldn't make a contractor send a garbage disposal back just because the package had one to few wire nuts in it. So I agree with TimNY's reply.
Installing a 15 amp circuit for a 20 amp device, no.
The common thing I hear from contractors who want to vary from manufacturer's instructions is "I have always done it this way", but if we are going to protect the public, the installation needs to be the way the manufacturer says so the warranties etc. stay in full force or effect; unless what they are doing is unsafe.