Any downside of booking an RT ticket as multicity?
 

I had to book a trip HYD-JFK-HYD. When I was booking it as a roundtrip however, I was unable to get the specific flight pair I wanted for the outbound (529 connecting to 203). The inbound was fine and giving me the flights I wanted, so I ended up searching it as a multicity:
HYD-DXB/DXB-JFK/JFK-HYD. Priced out the same as it would've been as a roundtrip and I was able to choose the specific flights I wanted so I booked it as a multicity. Connection in DXB is still 2.5 hours. I just want to make sure that booking as a multicity won't make checking bags through or getting BP/s for both segments an issue?
Any help is appreciated.

Thanks

Nope since there's no stopover and the underlying fare will be the same HYD-JFK fare

Indeed, I've seen that also. Normally when I want to spend a night in Dubai, but the connection is < 24 hours. It doesn't seem to show all the combinations.

Ive done this quite often when it doesnt show the specific flight i want as a pairing (usually because i want a longer stopover in dubai but still less than 24 hours).
No issues whatsoever as the underlying fare and pricing is the same.