I've had this work both ways; there have been times the UA codeshares on US metal were much cheaper than US offered them, and with the added benefit that standbys are done free-of-charge rather than for $25 (sometimes you have to remind the US GAs of that fact).

Likewise, there have been many times where the UA codeshare on the same US metal costs much more than the US flight, such as when I flew WAS-RDU a couple of times last year for football games. The US flight was $110 or so, whereas the UA codeshare was $1500.

It sounds like the OP is talking about taking US metal flights based on the airports involved. The only downside I know of to taking the cheaper US flight # is that if you want to stand by, it will cost you $25 (whereas with the UA codeshare, you get the UA free same-day standby rules). OTOH, that $25 standby seems to book into full Y IME, which can be a nice boost to EQM/EQS for little cost. You will not get UA lifetime miles, credit toward CR1s or 500's with either the US or UA flight #s on US metal.

On a US codeshare on UA metal (which can often be cheaper than the UA flight, IME), you do still get lifetime miles, and credit toward 500's; I don't recall if my experience was that you got credit toward CR1s.