What I believe is happening is bumble-bots is removing the vanilla roboport definitions rather than just changing them. This will break any mod that attempts to modify roboports AFTER bumble-bots. Bumble-bots SHOULD do this in data-final.lua. So if you rename my data-final.lua to data.lua and bumble-bots data.lua to data-final.lua it will make them run AFTER I make my changes.
My data-final.lua used to be a data.lua in 4.2.17 but Krastorio makes changes to bots in data.lua and I needed to move my changes after Krastorio's to change the bots to the way my mod offers for bot changes.
bumble-bots does this in data.lua:
-- get rid of mask for vanilla port to let the base graphics shine through
local vanillaRoboport = data.raw["roboport"]["roboport"]
for k, v in pairs({
"base", "base_animation", "door_animation_up",
"door_animation_down"
}) do table.remove(vanillaRoboport[v].layers, 2) end
Removing all definition of vanilla roboports, anyone who tries to modify a roboport after that will cause a crash.
If above makes no sense to you - join my discord and we can talk.
https://discord.gg/B9FJDndY
I may have time in 2 or 3 days to look at this and offer a more permanent solution.