Ah, but it's so convenient to use it I will try not using it next time, but for darkening things like the terrain when going deeper and deeper underwater I think it's a good idea to use it?
It's convenient but deceitful
It will not really make you learn colors and shading, but provide an easy and temporary cheat to do it. Eventually you'll end up (in a bigger, more complex piece) with more colors than the 256 old GIF limit and Pyxel Edit will simply not let you save your file above the color limit. Trust me I learned this the hard way when I first started...
But yes what you -could- use it for is to just darken, or in your case add a blue hue to the reflection, but only AFTER you've composed the scene with more limited number of colors.
Cause what you're doing now is, let's say you have 30 colors in your forest, the reflection will double that number cause it will add a new hue to all of them.
So yeah, start simple and forget about the opacity as easy as it makes things appear!