I just tried it out on v0.2.5c and it seems to be working as expected (images below), though I think I may see the source of your confusion: If you don't change the colours in the tool and also don't set a colour in pico-8, then it will appear to be reversed, because the default colours in this tool don't match pico-8's default. I can update the default colour selection in the tool so that's less confusing in the future.
I'm not sure what you mean by the alpha bit though, could you provide more detail or some code to show what you mean?
![fillp tool GUI showing a thin orange line on red bg fillp tool GUI showing a thin orange line on red bg](https://img.itch.zone/aW1nLzEwMjYxNDgxLnBuZw==/original/7XPP45.png)
![PICO-8 showing code corresponding with fillp tool's output PICO-8 showing code corresponding with fillp tool's output](https://img.itch.zone/aW1nLzEwMjYxNDgzLnBuZw==/original/h6%2BMqt.png)
![PICO-8 render showing output matching fillp tool PICO-8 render showing output matching fillp tool](https://img.itch.zone/aW1nLzEwMjYxNDg1LnBuZw==/original/TXUvL9.png)