I imagine the rent a room scheme is not open to you personally as you won't be living there, but would be open to your fellow owner. He could simply let the room under the scheme and pay your share of the mortgage with the money. I presume you trust him as you bought a property together.
There is no tenancy with the rent a room scheme-make sure you don't use a standard rental agreement that uses phrases like 'landlord' and 'tenant' because these don't apply here. There is a licence in place, not a tenancy. The rent a room licencee (the 'tenant') can be booted out at any time and is not covered by the Private Residential Tenancies Act (a good thing for the owner!).
The 10,000 tax free exemption doesn't affect other income so your co-owner shouldn't have a problem from that end and it would be fully legit this way as it is clearly still his PPR whereas it is not clearly still yours (as you'll be away travelling).
If your mate is not agreeable to the above (in my view the simplest solution) then maybe have a chat with an accountant (if no concrete advice comes along here) as you don't want to leave yourself open to a tax bill/stamp duty clawback etc.
An interesting tax question nonetheless....