I think it is hard to get an accurate picture of how the high/full fare compares to the upgrades at the last minute.
For example, even though many times last minute fares are in Y/B/M or other higher tiers, it is also possible that last minute fares include the lower ones.
I typically see at least 1 or 2 seats available for sale in F, meaning it will convert over to either seat for upgrade or for TOD purchase.
That said, if you are buying a full fare or YBM fare, you should automatically get it.
However, if you fall into the lower fare bucket, and you are not 1K, you'll wind up being out of luck.
While it may or may not be fair to the last minute buyer, the system is currently set up so that only someone who buys a full fare will trump the elites with the complimentary upgrade (presuming space is available).
This involves a whole slew of things, from inventory/revenue management, to appropriate software algorithm, to controls at the airport, which, honestly, I don't know if UA (or other airlines for that matter) can figure out and make work 100% of the time.