Technically the calculation is nothing like that, skill numbers are handled as integers and baseAbilityMod(7) doesn't return 1.255 anymore now that I've "fixed" it to emulate Underrail's rounding errors. But the insanity of this all is a whole nother topic...
Anyways, I changed the first case. Synergies shall be checked if (modifiedSkill <= skillcap) instead of <.
The second one will stay. I'm not terribly concerned if it warns early in edge cases. There could always be indirect benefits despite wasted synergy (synergies to other skills, feat requirements, derived stats, etc) so staying cool is left as an exercise to the user!
I know this is fairly useless for hardcore underrailers. The idea was to teach the synergy quirks to those who aren't as deep in the rabbit hole.

And I might redo the whole thing later. Listing all constituent parts of effective skill (skill points, base ability modifier, total synergy points, synergy points by contributing skill, skillcap, wasted synergy points, item bonuses) somewhere would be much better, but I doubt I'll find a way to display all that information without cluttering the page even more. Maybe hidden in a tooltip for the skill number.