The only downside I can see about booking (in UC) with an online travel agent is that you cannot select your seat during the booking process - but I assume once you get your booking ref then you can look it up on the Virgin website and select your seat. I see Opodo have better fares than VS but want about £7 to select a seat!
The main disadvantage of booking with an OTA is if you need to change anything after you’ve booked, as you have to deal with the OTA not the airline and they can be notorious for being difficult to deal with and adding fees.
So I’d only go for it if you’re absolutely sure you won’t need to make any changes to your booking.
But yes, the OTA will give you your VS booking reference and you can then select seats in MMB as usual.