Yes higher altitude has thinner air . EFI should should make some adjustments but they may not have it rich enough .
My scooter dealer has a scooter with the same EFI engine as mine but on a diff body , he installed an injector for a 250cc ( we both have 150ccs ) and had to get a plug for a 32I BMW since the wire was diff than that of the 150 wire . With a modded airbox and Cherrybomb muffler it was running at 13 to 1 fuel spectrum on a dyno that rated it at 12.5 HP at the rear wheel .
Most have a closed system to where only a dealer could mod the CPU instead of anyone with a home computer . I would check out
www.ecotrons.com and see if they have a larger injector or if their CPU with software will work on your Honda . If you buy their EFI kit you can set up the timing curve and option to have a RPM limit or not ETC .
I have seen 2 programmable modules that piggyback to a stock CPU in order to make it richer and remove RPM limit , but could not find a simple person or report on of using it on an Echarm like mine so I did not want to spend 200 on junk or fry anything