There's quite a few ways they could interact with that, the obvious ones being giving hard limits or soft limits. Alternatively, they could just make breeding stats generally more difficult, preventing the current exponential growth of single-stat builds.
They could also make some stats antagonistic, such that increasing one stat decreases some others. This would encourage specialist monsters that would nonetheless have significant weaknesses, while generally strong all-round monsters would become almost impossible to make. A logical extreme of this would be something like MBM's Complex Breeding mod, where inherited traits are in thematically linked packages, rather than individual traits.
Lastly, they could just embrace that some stats will quickly approach absurd values and design game mechanics around players having access to effectively infinite stats. For example, having monsters that reflect damage or reduce all incoming damage to a single point. Effectively making each different enemy type into a unique puzzle to be overcome, rather than just brute-forced with damage and health.
Either way, it's the sort of thing that modders could quite likely tweak post-release anyway. I fully expect that we'll see some kind of Complex Breeding-like mod for Project R at some point.
