The linear synteny view with all the polygons uses a render optimization where multiple drawing operations are batched into a single operation (multiple line drawing operations get a single canvas.stroke() and it draws a "polyline")

see

this does speed it up but it results in different alpha blending on chrome vs firefox sometimes with firefox appearing more "pale" due to the lack of alpha blending on the polyline not stacking up darker and darker alpha blends

options to address this could include

a) do nothing
b) gather user feedback to see how much it matters
c) remove the optimization, should "fix" it
d) fix it some other way that preserves polyline, or only remove polyline on firefox
e) don't use the alpha channel at all, and just always use flat colors, or use flat colors by default
f) see what the situation looks like after implementing other synteny coloring options

those are not all mutually exclusive...