I applied for the H1B after 221g was issued (pending DS5535) for IR1. The attorney representing my employer/me is aware of the ongoing IR1 petition and didn’t see an issue. Luckily, from that front, I didn’t encounter any problem. My intension is still to return to Canada to complete consular processing for IR1 once AP is completed and I shared that upfront. Not sure if this was explicitly mentioned or was even asked for the petition.
One good thing to know - as Canadian, I am interview exempted, meaning I can directly cross the boarder and get my visa stamped there. I was dreading yet another interview, cause I still have ++ PTSD post montreal interview.