Trying to reconcile the whole regeneration thing is like trying to ski uphill.
Yep, particularly since in the Davies era it seemed like the production had dropped the idea of a set number of regenerations.
Why because of the Master? We know that the Time Lords gave him more regenerations in the hope he'd fight the war for them, but he raan off instead. But there's nothing to suggest that RTD dropped the regeneration limit.
Nothing definitive but in Sarah Jane, 11 states that he can regenerate 507 times, suggesting to me that the limit of twelve was being wafted away in a similar fashion to the smooth headed klingons in Deep Space Nine.
Also the only time RTD wrote for Matt Smith i believe.