@Richard Wilson yeah the partial cycle behavior is actually one of the nicer properties of supercaps compared to lithium — there's no memory effect and no chemistry to degrade, so partial charges are genuinely fine, not just "acceptable." The aggressive front-end charge curve you're describing is real; supercaps absorb current fast when they're depleted, then taper as they approach capacity, which works really well with intermittent solar because you're essentially harvesting energy in short bursts all day rather than needing a sustained charge window.
For a 5W panel with a GNSS + sensors stack, the main thing I'd watch is whether your panel's output voltage is being regulated before it hits the supercap input — you want current limiting in there or a short burst of strong sun could push input current higher than the cap's rated charge current. The Power Kit handles the programming/power side cleanly but it's worth double-checking what your solar charge controller is outputting.
The rail voltage logging idea is genuinely the right move here. A cloudy day log at 1-minute intervals would show you your effective floor voltage and whether the cap is recovering fast enough between cloud gaps to keep your stack alive through the quiet periods.