Recurring Dream and Mr. McCallahan Presents may reference CC1 levels in terms of content, but both of those levels also reference other CCLP3 levels as part of Chip's memory as described in the storyline. MMP also referenced a number of JL1 levels that weren't in CCLP3 (Japanese Game Show, Deliverance, Before the Rainstorm). If a player goes through MMP without playing these levels, the references will just sail over his head. I think it'd still be acceptable to include CC1 as part of the "canon," but seeing a title like "Oorto Geld II" is a bit more jarring for someone who's never played the original game than seeing a reference to original game content within an actual level that won't be recognizable to that player.
As for Yet Another Puzzle and After the Rainstorm, these levels weren't referencing anything that preceded them, not even in the context of their original set, so I don't see an issue here.
As for Yet Another Puzzle and After the Rainstorm, these levels weren't referencing anything that preceded them, not even in the context of their original set, so I don't see an issue here.