As the linked post says, Lon/Lat is generally easier to deal with b/c it matches to X/Y (and the North/Up way we look at maps). But you still have annoyances. For instance Lon goes 0-360 but Lat goes -90 to 90. This is also mathematically inconvenient
Add on top of that the X-Y coordinate on images generally have the X flipped and starting at the top left corner. So changing to Lon/Lat doesn't fix everything.
What I personally lean towards now is converting everything on read-in to a South/East coordinate system so it matches the flipped X-Y of images (like GeoTIFFs) and just always working in that system. Image manipulation, drawing to screen, output etc. - those systems/libraries I can't really modify myself. Everything else I can manipulate in whatever coordinate system I want. So it makes sense to choose the most convenient. Plus only dealing with positive coordinates is a big plus.
That all said, I'm a total noob and I have no "geospatial" background (just writing some software to deal with rain data right now) So this isn't pro advice. I'd just be curious what others think