What you are describing is called "switchover" transient - in essence, there are at least three factors in play: a) synchronization issues between the sinewave (or as close at it gets with the generator) waveform and that of your AC mains, b) ramp-up artifacts of the generator when it (or UPS) kicks in, and c) control circuit problems that governs the switchover. The "steady state" performance of your power conditioner is of little importance here - its transient response is what matters. This article from Repeater Builder provides good explanation: https://www.repeater-builder.com/backup-power/ups-test.html Your regular surge protector will ignore such artifacts, and likely your typical power conditioner will do so as well.
Tooting my own horn, our filters https://www.onfilter.com/ac-emi-filters-af-series do deal with such artifacts - at the factories for which they were designed such glitches may cause very serious problems rather than just an inconvenience of flickering light or a crackle.