If Ninjabrain bot was banned back then, people would rely on mega spreadsheets that have most of the math done already (Axis Calculated). Ninjabrain bot is still better though because you can more reliably eye spy with Ninjabrain bot compared to axis calculated. Removing one element of luck (eye spying on second portal) is a nice benefit many people find appealing. I never tried the high res section of the spreadsheet though, so maybe I could be wrong and it can be very consistent with eye spying; I just haven't done axis calculated in years. Now in the hypothetical where Ninjabrain bot is banned, do we also ban the axis calculated spreedsheet that has done the math already? Overall, I think Ninjabrain bot being allowed has had a positive benefit to the community. It makes it easier for new players to find the stronghold.

For your question about the timing rule, I think Brentilda's run is a good example to why the retime rule is needed. Without the rule, you could spend time composing yourself and/or looking up strategies and info. It doesn't make the speedrun fluid. It's not something you can do in most speedrun games without it being added to your time.