Yes, Lord Rat sucks as an opponent in many situations. He/She will, quite often, buy a crapload of one card (Counterfeit is a prime example), but never use that card properly. And you've found another example--making a perfectly good buy of Chapel, and then "intentionally" using it as badly as humanly (robotically???) possible. It does make the games with these cards/behavior no fun at all. But pretty quickly, you will likely do what I do...I quickly resign when LR starts to self-destruct. No fun at all playing a game that I cannot possibly lose.
My guess is (a) That Chapel is an exceptionally difficult card to code for, and (b) that fixing this is probably very low on the priority list. I don't think it's a bug, per se. It's just dreadful gameplay, and that is due to how some cards are programmed to work inside of LR's games. (You will see LR buy a bunch of Banks, and then play the banks before
playing any other Treasures...I've been hoping for that particular fix since forever.)