Matthysse, who has 39 wins including 36 by knockout against four defeats, won the vacant WBA belt after beating Thailand's Teerachai Sithmorseng in January.
"That's Manny's decision. Manny has told me Buboy will be handling the training on this fight", Pacquiao adviser Michael Koncz told ESPN.
One reason Pacquiao could be working with Arum on the PPV and North American distribution of the Matthysse fight, could be due to wanting a fight with Vasyl Lomachenko.
Reports surfaced in early March that Pacquiao had already chosen to fight Mathysse, with his initial choices being between the Argentinian WBA champion and former two-division world champion Danny Garcia and the target date being June 24th.
Asked about the reason Pacquiao chose to make a change - without notifying Roach - Koncz said, "There was some concerns Manny had in the last fight and some statements Freddie made to the media that Manny wasn't very pleased about".
Though rumours of friction are rife, Pacquiao and his team insist they have no issue with Top Rank and intend to work with Pacquaio's long-time partners for a fight in the autumn.
"We are very pleased and privileged that ESPN will be part of this fight because of the tremendous viewing audience we had for the Australian fight", Koncz said.
Although Top Rank boss Bob Arum will have no direct hand in the event since Manny Pacquiao Promotions will be handling the title bout, the American promoter will still be involved in the television distribution of the bout in the U.S., according to Koncz.
Filipino Pacquiao, 39, last fought in a unanimous points loss to Australian Jeff Horn in July past year. "Hopefully, this fight with Matthysse is a big success and Manny is victorious, and then we can see if we can do a fight with [Vasiliy] Lomachenko with Top Rank in the fall". "He deserves it and he's wanted it for some time now and whenever you get a chance to fight Manny Pacquiao, you've got to be willing to go to the moon if it's going to take place there", Gomez said.
This is close to a toss-up fight for me, as both guys are clearly past their prime and we know to expect the unexpected when guys no longer have their pure skill sets.