No it's been paid for by the teams. At least that's been my understanding from following the manager of Team Hitec, Karl Lima, on Twitter.Did they ever? Surely the pre-race testing - and mid-race testing for GTs - is organised, and paid for, by race organisers and UCI. Otherwise, the whole system could fall apart.
Increased budget item is part of new reality for peloton.
Question no. 11 in this FAQ also deals with the costs of the protocol: