Well, the head/tail crossfade that we use for seamless dubbing over the splice (and smoother transitions overall) is always running, so that's what you're hearing in the initial Press of the play button, except the fade down part of the loop tail is of course muted for initial play, so you just get a quick fade up. I think the crossfade is something like 5 ms for non-tempo mode, and 20 ms for tempo mode (to account for external MIDICLK jitter/noise).
The whole point of this method was to allow continuous reverb type sounds to dub over the loop boundary without any audible seam. The previous TF Looper always did a quick fade down then back up (not even a crossfade), so it wasn't capable of this at all. I didn't come up with anything other than this fade for initial transitions to Play though….. I suppose the best thing you could do for Record to Play transitions is actually transition from Record to Dub instead. Then turn off Dubbing after fading your input signal down.
The clicks on multiple play-retriggers sounds like a bug to me, nothing is supposed to click or pop with the Looper….. we wanted it to be as smooth as possible.
There may be some more sophisticated DSP tricks that we could employ in the future for these initial Play transitions, like running a zero crossing detector and always starting close to zero crossing, but I'm just spit-balling really, because I'm probably not going to do anything like that in near future.