It seems that byobu triggers a known bug with tpm which then fails to load any plugins. Fortunately there is a simple fix, in byobu’s .tmux.conf change your plugin formatting like so:
set -g @tpm_plugins ' \
If using the XDG directory convention, this line is also needed in .tmux.conf:
set-environment -g TMUX_PLUGIN_MANAGER_PATH "~/.config/byobu/plugins/"
It seems that byobu‘s defaults don’t play nice with emacs, eating important key sequences such as <C-h> and breaking color schemes. Adding the following line to ~/.byobu/.tmux.conf fixed the issue:
set -g default-terminal "screen-256color"