Yopappaman,
They used to...
Based on the posters initial phrasing, they seem to have made a recent purchase... more likely than not this would have included an EB709XC style controller not the older EB809 (even though they use the same Micro controller, they are very different)...
I believe the kits from the past few months (2-3) have been shipped with EB709XC controllers they received a while back, the 809 was phased out by the supplier with little if any notice to them... certainly no explaination of the lack of programability and other such features... the kit companies (ebikekit, etc) are targeting the "masses" who will never try this type of upgrade or fine tuning so it wasn't a major point of issue to them.
I've been advised they will be offering the either the EB206 or the EB209 models in the near (maybe a month?) future and those will be programmable and adaptable just as they are now, but those include the 116 CPU...
The EB709 and EB712 from ebike.ca are also not yet programmable (I don't even think the "routine" needed for changing settings is in the firmware on these chips) - heck they received a batch (a large batch) which needed all the chips removed and replaced (I hope that is public knowledge, I swear I remember reading that in a thread somewhere) because the darn vendor (China) wouldn't ship software to reprogram the existing chips!
I suppose my point is, if you want to be ANGRY or IRRITATED with anyone over these "non programmable" controllers.... be mad at the Chinese who just in essence "pulled a fast one" on everybody. Their logic (imho) is that if the dealer can't just reprogram, they must order MORE... In truth without the ability to program these controllers a dealer can't possibly calibrate them to a new motor... so when the next gen, revision, evolution of motor arrives... these may or may not be compatible and efficient - luck of the draw, again requiring more purchases from the chinese vendors.... but what they are going to find out is they have a bunch of controllers not a single vendor here in the US wants to purchase and will not order again
All that said and out of the way, you can still mod these... it's just all back to the hardware hacks of yester year that got us all started to begin with. As luck would have it, we have (methods, knuckles, lyen, arlo1, steveo, etc, etc) had alot of time with the 846 CPU and the EB8XX series boards and the PCB layout isn't much different in any way that matters... R12 mods still apply for altering the LVC (I think it still uses a 1.2K resistor too), shunt mods still apply (or resistor mods across the shunt return to the MCU)... we just lost the ability (only with the EB7XX series) to fine tune things using software...
I hope that answers the question well enough
-Mike