Hehe thanks! During phase 2 (buck) every time the buck mosfet switches off, which is very often, the bootstrap cap is recharged, so you don't have to do anything special. But in the boost phase the buck mosfet is on continuously, it just lets current through, so the cap will not recharge, you have to "manually" nudge it.
The new connector are fine, also it's just 5A so you can use more flexible wire than the garden hose stuff that usually goes with XT60
The connector on the right may be the wrong way around, as the wires come out on the board side. But there's only ceramic caps there, so if you check the height, I mean if the top of the caps is lower than the bottom of the wire hole in the connector, then you'll be able to stick the wire in and it could be practical since it makes your board shorter, without the wires sticking out the sides...
Anyway I think you'll solder the connectors manually so you can put them facing one side or the other, but I wonder if the two "BAT" connectors (which you should label properly btw) could move a little bit to allow turning the screw terminals on the left to be rotated 180° if needed...
Also these screw terminals are pretty much square, you can also rotate them 90° so wires come out "up" or "down" instead of "left" or "right (when looking at the pcb on screen) if that's better for fitting it all together mechanically