One key take away is that OSM edits need to be made that reflect all aspects of a way or node, and not how any particular application needs/renders the data.

This issue is something you should take up with the Map tool. They need to be more tolerant of unexpected tags.

I did not change the name. The naming is consistent with the key=ref tag document in the wiki. Be sure to read the part about
'It may seem redundant to tag route refs on both ways and relations, but do not remove a ref=* tag from a way just because the way is a member of corresponding route relations:'

The Exit is signed as "49" and not some mile marker which any local would be hard pressed to tell you.
The Junction:ref=49 is also correct.

As for the destination, there are proposed tags for that, but they are used on the exit node of the way where it meets the lower category roadway, so in this case, the last node where the junction meets NY 78. Once again those tag usages are for the Viewing application to interpret.

One final thing, you should send people internal messages about questions, not comments on the way. I would never have seen this if I hadn't be looking for a specific email about another topic. Other than the email, this doesn't show up as a message for me in my inbox.

NYS Thruway numbering does not match Interstate highway norms because the Thruway had been completed for 2 years before it was added to Interstate 90.
https://en.wikipedia.org/wiki/New_York_State_Thruway

My edit consisted of removing a stacked way for the exit which was stacked on another way that referenced the same exit. The last previous update had been 9 years prior, and did not reflect changes implemented during the removal of staffed toll barriers.

It still isn't rendering. What change did you apply to the relation before you closed the the issue? I do see several issues on the US side of the lake that I am not sure how to fix. namely that the relation is encompassing spaces that include bays and rivers which are separately named features and not part of the lake. the view I still see the problem with is: https://en.wikipedia.org/wiki/Buffalo,_New_York#/map/0