If you take the 2:55 vs 3:35 (that is, slowest times for the fastest and slowest examples)
It breaks down to
175 seconds vs 215, which comes out at approx 19% difference.
The reason we are seeing this an no one has queried it with other flash carts is you don't notice it on other flashcarts due to the often very short programming times related to tiny ROM images. For example, 19% difference between 2 x Everdrive or SD2SNES etc could result in a negligble difference. If you time say 5 seconds to program a cart on a SNES or Megadrive, would you honestly notice between 0.5 sec to 1 sec difference to anyone elses cart - almost definitely not, and in fact I've never seen anyone report that as a problem because no one else has noticed it up until now, and that's because the games on the neo geo are obviously much larger and this technology just hasn't really been used for games this large before.
An alternative is if you get a cart you think is too slow for you, just stick it on eBay and buy another - you will get 100% asking price (maybe more) due to PayPal on eBay! The reality is the manufacturer does not tell you in advance which flash ROMs will perform at the better end of that 20% tolerance and which perform at the slower end of that 20% - so what are the Neo SD team expected to do? I would suggest when they update their website with specs etc, they just clearly state "average programming time for KoF2003 is ~3 minutes, but it could be up to 20% more or less and performance can be affected by micro SD speed".
The other alternative is for Neo SD to start using even faster lower tolerance chips and increase the cost by a hefty percentage - wild guess, additional 100 euros or more, and maybe then it might have 10% tolerance still.
I am sure if there's any way to improve performance in future, they will let us know. Their whole aim from the start here was to make this as stable and as fast as possible, and as said before we are all better off than where we started because the 'faster firmware update' was around 30% faster to start with. Beyond that, what else would you expect, a recall to swap out the ROM chips with faster ones (that would involve massive costs and no one in their right mind would do it)???? For one thing, think of the cost of the chips alone - lets say 10% of them perform 20% faster than others, does that mean they have to start binning or selling 90% of the chips they buy in, and the logistics behind testing those chips in advance would be an absolute nightmare.
I did suggest that if people start getting stressed about this that the next firmware update should slow all carts down to equal footing - that sounds counter productive, but it seems to me like people are getting stressed about that 19% and it might stop the concerns here.
Sorry if that sounded like a rant, it wasn't supposed to be. It just feels to me like this thread has turned into another thread to p*** off the Neo SD team.