Actually I think might have found a potential solution, that comes in "A Town Called Eternity". The Master, after suffering from major burns during the events of Planet of Fire, discovers the Fountain of Youth and restores Tremas's body.
The Master stood in the fountain of youth, the flow of water passing over his entire body. He could feel the invigorating properties of the water working their way through him, strange energies even a Time Lord could not understand. He sighed ecstatically as his body, that feeble humanoid body too weak for a being such as he, was restored to full health.
Could it perhaps be that the Fountain of Youth restored him physically back to a point in his timeline where he still had the Trakenite body? I don’t think that’s the intention (in fact this was written several years before The Velevet Dark) but considering the Master himself doesn’t understand how it works, who knows?