Is there any reason to use a Nyokimon and a Punimon, and not just go for 2 of either one?

I believe I may have discovered why. 2 Firamon don't do so great against Whamon.

I believe I only made that a part of the initial route because it was way more common for 1 of each of those to spawn rather than 2 of the same to spawn on the map. It is possible that 2 Nyokimon or 2 Punimon could work in a run but I was never able to test it myself.

I've noticed them spawning in packs, actually. It could just be RNG tho

Speaking of the guide, I've been meaning to ask how much training I should actually do.

depends on the season, during spring just train hp and attack at least 5 times each. you really want to max both of them out for each evolution stage though, unless you think you're short on time and want to rely on RNG.

during summer max out hp, try to get a good balance of atk and def, will be pretty easy to tell what that is by maxing out attack first and then raising defence a few times.