I didn't miss anything you said, you're just incorrect. Tomorrowland was not completely shut down for the 1998 refurb. It was done in pieces for the bulk of the construction and only completely closed the last few of months of construction to wrap things up. I can show you at least 3 videos on YouTube that prove this. One of them early in the construction where people are on the still operating Peoplemover filming Innoventions and Space Mountain behind construction walls, and one of them taken in January of 1998 showing people walking through Tomorrowland with walls up around the now Buzz building and Star Tours.
Actually, let's think about how the crowds were AFTER the opening of GE:
Disneyland Park has reached capacity as of 2:30 PM on December 27th. Read on to find out how this might affect your vacation plans.
allears.net
Yes, it was the busy holiday season, but the addition of GE still didn't prevent it from happening. Removing Tomorrowland would have been a nightmare back then.
Now advance to today. With the reservation system they can mitigate the crowds ahead of time. People don't notice changes when lands are added because they just add more reservation capacity.
It's much different when you take space away. As I said before, they would need to reduce the reservation capacity and people WILL notice that. MK holders already complain that it is hard to get a reservation within a two to three week lead time. Imagine if they reduced them. Social media and the instantaneous spreading of information has changed how Disney operates. The outcries are heard much quicker and deeper. (See AI portraits)
So no, I still don't believe that they would close 1/3 of Disneyland for multiple years to redo Tomorrowland, even with the existence of GE now. In fact, I don't believe a TL overhaul will happen in my lifetime.