As Guy Betsy states, there's no problem in having both rooms in your name. I often do this. According to Hhonors rules, you are entitled to points for two rooms as long as you get one folio for both rooms upon checkout. Just make sure the second room is transferred to your room's invoice upon checkout. This sometimes seems to cause the front desk agents a few problems, but they should all be able to do it. You're only entitled to Diamond benefits for yourself and one other person in your room. However, up till now, I've always been granted the benefits for both rooms.

As you state, the hotel may consider you have double booked by mistake. I have occasionally had the hotels e-mail me to confirm that I actually do want to reserve two rooms. Suspect that this is when they're fully booked. You could always ring them to confirm the two reservations and if you want request rooms on the same floor.