It is ofcourse risky but I would not call it a "very very bad idea". I saved almost Rs. 30k which I think was worth taking the risk. While I was travelling BOM-MNL (via HKG with HKG-MNL on PR), I had checked with 9W and was told that if 9W flight on BOM-HKG is delayed by more than 2 hours, it will take responsibility for my onward connection, even if the next ticket is on a different PNR and a different airline. So it seems, airlines have some informal rules which they may or may not follow depending on the situation. In general, I have seen that airlines in Asia are mostly accommodative, so took the chance. I probably would not have done it for Europe or US.

To update on my experience, the typhoon situation fortunately did not turn out to be that bad.

While checking-in in Manila, I checked with PR if they could check my luggage to BOM even if I was holding different tickets (MNL-BKK on PR and BKK-BOM on 9W) on separate PNRs. Surprisingly, they did and when I landed in BKK, a 9W official was for me and escorted me to the transfer area. So essentially, PR could link the two PNRs and through check-in my luggage!