Ok, this has been kinda nagging at the back of my mind. I came across this several months after purchasing the Anthology:

From BethBlog:

How more specifically are the DLCs not compatible with the disc version? I had installed GOTY disc version, copied the DLC ESPs + BSAs from "Program Files / Steam / steamapps / common / Oblivion / Data" to my regular game folder. Upon starting a new game with only the DLCs and Unofficial Patches installed I got all the excessive New Quest spam at the beginning (now I don't get any spam since adding SM Plugin Refurbish to my setup). Unfortunately, searching Google and the forums hasn't provided any more details than the info that's quoted above.

Has anyone else tried using the DLCs from the Steam version with the disc version, and without giving any spoilers, has all the content worked as normal? I guess it's not too big of a deal if the DLCs don't work and I could just play without them since they seem fairly small compared to something like OOO, UL, or Better Cities. Just wanted a little clarification, this has been kinda bugging since reading that blurb.

Have you read http://www.gamesas.com/topic/1473087-faqs-for-the-elder-scrolls-anthology/?

Yep. Unfortunately, it only reiterates the above quote from BethBlog.

FAQs for The Elder Scrolls Anthology:

That's where he got the quote about the DLCs not being compatible.

I have no idea what they're talking about in that Bethblog. I can see no reason why the DLC would not be compatible with any version of the game, disc or digital. If those annoyingly spammy DLC messages (what on earth were they thinking?) show up when you enter the game, then I think the DLC ought to be ready to play.

Yeah, I figured if the messages show up then they're ok, though I wouldn't put it past Valve to talk Bethesda into modifying addons so they only work with steam... Anyway, thank you both for the replies

As for the messages, SM Plugin Refurbish not only gets rid of them, but allows each of the DLC quests to be started in a more immersive way:

http://www.nexusmods.com/oblivion/mods/11474/?