When I open a file-chooser window (floating), it opens in a way that the superior part is out of the screen, as shown below.
Is just noticed this only happens in my secondary monitor with lower resolution:
➜ xrandr G conn
eDP-1 connected primary 2256x1504+0+0 (normal left inverted right x axis y axis) 285mm x 190mm
DP-1 connected 1920x1080+2256+0 (normal left inverted right x axis y axis) 476mm x 268mm
Is there a way to configure the file-chooser (or any floating windows) so it is always centered? Or at least to fit in the lower resolution?

I had the exact same problem. I fixed it by restricting the max size of floating windows by adding the following line to my i3 config file:
However this does, as it says, restrict the maximum size, so it will stop a floating window being opened larger than that size as well as also not allowing you to resize it any larger than that manually, which might not be what you want. It's what I use though.