I think this is a little complicated. Geoffrey Samuels suggests that whilst Pabongkha's actions went against the Thirteenth Dalai Lama's spiritual interests, they did in some way fit in with his political aspirations of making Tibet a more organised centralised state. Along with making Geshe degrees more rigourous, setting up a standing army and other measures,Sherab wrote:If forced conversions happened while the 13th Dalai Lama was alive, did he issue an order to Pabongka Rinpoche to stop those conversions? If no, why? (I don't think distance is a good explanation if the answer to my question is no.)
He goes on to say:Civilized Shamans p51 wrote:Again in the religious sphere, the lama P'awongk'a Rimpoch'e, acting in association with the Dalai Lama, instituted a campaign to convert non-Gelugpa gompa in K'am to the Gelugpa school, by force where necessary.
Civilized Shamans p545 wrote:P'awongk'a Rimpoch'e thus stood in a complex relationship to the 13th Dalai Lama, and in fact the two men were not personally close. The 13th Dalai Lama, like the Great 5th, was interested in the Nyingmapa, and Dzogch'en traditions, and received teachings from Rimed lamas such as Terton Sogyal (also known as Lerab Lingpa: see Smith 1969a:17 n.59: Mullin 1988:37). His own orientation seems to have been open-minded and eclectic, and he was not identified with P'awongk'a's conservative and traditionalist faction. Nevertheless P'awongk'a was in some respects the logical expression in the religious sphere of the transformation that the 13th Dalai Lama was trying to bring about. Had the Lhasa government ever succeeded in turning Tibet into an effective centralized state, the Gelugpa might have continued to move in this direction and might have gradually eliminated the other Tibetan religious traditions in favor of a well-controlled academic and clerical version of Tibetan Buddhism.
One also has to bare in mind the other issues happening here. In complaints made about Pabongkha by Rimed lamas such as Jamyang Khyentse, Pabongkha's sectarianism was inextricably linked to his ghost worship. In response to these complaints, the Thirteenth Dalai Lama wrote to Pabongkha and told him to stop. Pabongkha wrote back saying that he was in error and he would stop. He didn't.