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 LN doesn't record every TX on the base layer. Just the opening and closing of a channel. 
 Of course, I don't understand your point though.

I'm not suggesting the lightning payment directly pay fees for that timestamp. Peter would accumulate lightning sats received in this way and periodically loop-out into his opentimestamps wallet, which would then help pay for opentimestamps on-chain transactions in the future. 
 Yes, that's exactly what I do with donations.

Accepting LN for speeding up transactions makes sense and I'll probably do it at some point. It does require a bunch of code to do well though.