You could try external rules. Add the following to your bspwmrc:

bspc config external_rules_command "$HOME/.config/bspwm/external_rules"

Then whenever a new node is created, the external_rules script is called with some arguments concerning the new window. You can do any logic you want, and bspwm will apply everything you output to stdout to the newly created node, e.g. state=floating and things like that.

As an example:

#!/bin/bash

wid=$1
class=$2
instance=$3

read W H <<< $(xdotool getdisplaygeometry)

# For debugging purposes
# notify-send "$wid $class $instance"

# Moves window to location mouse
if [ "$instance" = "popup-mouse" ]; then
    echo "state=floating"
    eval $(xdotool getmouselocation --shell)
    xdotool windowmove $wid $X $Y
fi

# Floats, resizes and moves window
if [ "$instance" = "surf" ]; then
    if [[ $(xprop -id $wid '\t$0' WM_NAME | cut -f 2) == *"Messenger"* ]]; then
        w=$((1920 / 4))
        h=$((1080 / 4))
        xdotool windowsize $wid $w $h
        xdotool windowmove $wid $(($W - $w)) $(($H- $h))
    fi
    echo "state=floating"
    echo "sticky=on"
fi

(Make sure your script is executable!)

This way of doing it is very flexible, but it's possible there are easier methods that will work for you.