I think there's a big difference in drawing inspiration from a story ("Brave New World," "Pull Me Under," "To Tame a Land") or retell it is fine. Especially since the subject matter in those songs is pretty obvious in most cases. But when lifting direct passages, something like quotes in the lyrics page ("Rime of the Ancient Mariner," "Xanadu") or a small credit to source material should be included somewhere.
Its not a huge issue, no, but it can seem a bit sneaky and dishonest, even if the artist comes clean about it in an interview or something. The phrasing of some of the 6DoiT lines are too similar to that journal. Its entirely possible (and pretty likely) that Petrucci read that specific one. After all, he's said he looked up journals when writing "Voices," making me wonder if lines like "spider in the window" etc. are lifted from books as well. :/ I still love 6DoiT but it makes me a bit sad knowing some really cool images or terms weren't his.
Its not really legally stealing, but I don't think that means it gets a free pass. Just some official acknowledgment in the album booklet would be fine.