Interestingly, while these CyberComics COULD have been used to direct readers to buy the printed ones, it was in fact the printed comics that were used more heavily to drive readers to the webcomics! Gambit #12 made direct reference to the the Gambit: The Hunt for the Tomorrow Stone CyberComic, and I recall quite a debate among the Marvel Chronology Project board of directors on how, or even if, we should handle presenting that new twist to continuity.
(I might point out, though, that these Messenger comics were definitely NOT in continuity. In the storyline shown here, there were any number of disconnects with established continuity, the most obvious of which was that they changed the name and origin of Dr. Doom's mother -- that's her in the last panel. In retrospect, I think this was deliberately done to show that these stories weren't "real" compared to the ones you had to buy.)
Although I don't think there are many people working at Marvel today who worked on any of these cybercomics, I continue to get the impression that their early not-great experiences there have colored the company's view on webcomics.