There are three types of blues in vanilla, so I prefer to have one turned into teal. This doesn't make much of a difference and shouldn't collide with any new graphics.
This
WILL most definitely collide with all converted graphics.
Imagine you have a picture with a gradient from light to dark blue somewhere... if it was hand-drawn, the author would (mostly) use only one shade of blue (out of the three you mentioned). After changing the palette the intensity may change a bit, but gradient and most importantly color will be preserved... so changing vanilla assets is OK.
Now take your average modding resource, converted from some cool internet graphics.
Let's say it has a blue gradient.
You've used your favorite image-processing software and it has decreased the color depth to 256 colors according to xcom palette to the best of its abilities.
Very likely, it has used all 3 blue gradients in the process.After changing the palette (let's say one blue to teal and second blue to cyan)... you'll get a horrible mix of blue, teal and cyan barely resembling any gradient attempt at all... and kill my eyes slowly in the process.