Took me a few minutes to figure out that the external_bar setting needs to be set before top_padding, bottom_padding, etc. in yabairc. So something like this works as expected:
yabai -m config external_bar all:0:26
yabai -m config top_padding 5
yabai -m config bottom_padding 5
yabai -m config left_padding 5
yabai -m config right_padding 5
But something like this won't respect the external_bar setting until after toggling the padding on and off (e.g., with yabai -m space --toggle padding):
yabai -m config top_padding 5
yabai -m config bottom_padding 5
yabai -m config left_padding 5
yabai -m config right_padding 5
yabai -m config external_bar all:0:26
That is not intentional and I don't immediately remember why this would be the case. Sounds more like a bug rather than an anomaly that has to be documented.
Fixed on master.