This is indeed an interesting comparison, even if it is on a biased platform.
In Absentia is the only Porcupine Tree album that intrigued me. It is certainly a good album, and in my estimation, PT's best. On the other hand, all of Opeth's albums intrigue me. Damnation is, again in my estimation, their least involving album. In Absentia is a bit less restrained than Damnation because of Damnation's pre-existing, outlined nature. The instrument work on Damnation is far superior to that on In Absentia. The styles aren't directly related, but they do, at times, faintly echo one another.
Any view on this topic is valid, though. Whether you think both albums are great, and favor one over the other; whether you think one album is far superior to the other; whether you are thrilled with both albums; whether you are disappointed with both albums, it's all understandable and defensible. Both these albums have at times made me feel empathy, antipathy and rapture.
My vote went to Damnation for the justified fear of it losing on it's home ground. That and the instrumentation of Opeth is always inspiring.