The patch does not seem to do anything: does not break manual tiling, does not fix layout loading.
(I did check that the changes to paned.py actually get compiled and used, e.g., playing with ratio produced bad results.)
So at least you can probably drop deprecated Gtk.(V/H)Paned if you want.

Launching a layout in terminator in either case does not produce any interesting logs (in fact, their were the same logs), see below.

(By the way, playing with ratio in paned.py (e.g., I set ratio=50.5) produced somewhat similar bad results for manual tiling: when splitting to bottom, the old pane gets fullscreen on top, after closing it you can see the new pane. Might there simply be some miscalculations of ratio/size on layout loading?)

UNINTERESTING LOGS (only the first ~7 lines seem to be relevant, the rest is just the result of consequent strokes/mouse movement):

LayoutLauncher::launch_layout: We have takeoff!
LayoutLauncher::launch_layout: Clicked for bredis
str::spawn_new_terminator: Spawning: /home/john/bzr/terminator/./terminator

** (terminator:8529): WARNING **: Binding '<Shift><Control><Alt>a' failed!
Unable to bind hide_window key, another instance/window has it.
Window::on_window_state_changed: Window::on_window_state_changed: fullscreen=False, maximised=False
ConfigBase::get_item: ConfigBase::get_item: title_hide_sizetext found in globals: False
ConfigBase::get_item: ConfigBase::get_item: title_use_system_font found in globals: True
ConfigBase::get_item: ConfigBase::get_item: geometry_hinting found in globals: False
ConfigBase::get_item: ConfigBase::get_item: focus found in globals: click
ConfigBase::get_item: ConfigBase::get_item: focus found in globals: click
ConfigBase::get_item: ConfigBase::get_item: cursor_color_fg found in profile default: True
ConfigBase::get_item: ConfigBase::get_item: title_hide_sizetext found in globals: False
ConfigBase::get_item: ConfigBase::get_item: title_use_system_font found in globals: True
ConfigBase::get_item: ConfigBase::get_item: title_transmit_fg_color found in globals: #ffffff
ConfigBase::get_item: ConfigBase::get_item: title_transmit_bg_color found in globals: #000000
ConfigBase::get_item: ConfigBase::get_item: title_transmit_fg_color found in globals: #ffffff
ConfigBase::get_item: ConfigBase::get_item: title_transmit_bg_color found in globals: #000000
ConfigBase::get_item: ConfigBase::get_item: show_titlebar found in profile default: True
Titlebar::get_desired_visibility: configured visibility: True
ConfigBase::get_item: ConfigBase::get_item: show_titlebar found in profile default: True
ConfigBase::get_item: ConfigBase::get_item: show_titlebar found in profile default: True
Titlebar::get_desired_visibility: configured visibility: True
ConfigBase::get_item: ConfigBase::get_item: show_titlebar found in profile default: True
Titlebar::update_visibility: showing titlebar
ConfigBase::get_item: ConfigBase::get_item: title_hide_sizetext found in globals: False
ConfigBase::get_item: ConfigBase::get_item: title_use_system_font found in globals: True
ConfigBase::get_item: ConfigBase::get_item: title_hide_sizetext found in globals: False
ConfigBase::get_item: ConfigBase::get_item: title_use_system_font found in globals: True
ConfigBase::get_item: ConfigBase::get_item: title_inactive_fg_color found in globals: #717171
ConfigBase::get_item: ConfigBase::get_item: title_inactive_bg_color found in globals: #ffffff
ConfigBase::get_item: ConfigBase::get_item: title_inactive_fg_color found in globals: #717171
ConfigBase::get_item: ConfigBase::get_item: title_inactive_bg_color found in globals: #ffffff
ConfigBase::get_item: ConfigBase::get_item: show_titlebar found in profile default: True
Titlebar::get_desired_visibility: configured visibility: True
ConfigBase::get_item: ConfigBase::get_item: show_titlebar found in profile default: True
ConfigBase::get_item: ConfigBase::get_item: show_titlebar found in profile default: True
Titlebar::get_desired_visibility: configured visibility: True
ConfigBase::get_item: ConfigBase::get_item: show_titlebar found in profile default: True
Titlebar::update_visibility: showing titlebar
ConfigBase::get_item: ConfigBase::get_item: hide_on_lose_focus found in globals: False
ConfigBase::get_item: ConfigBase::get_item: cursor_color_fg found in profile default: True
Window::on_window_state_changed: Window::on_window_state_changed: fullscreen=False, maximised=False
ConfigBase::get_item: ConfigBase::get_item: title_hide_sizetext found in globals: False
ConfigBase::get_item: ConfigBase::get_item: title_use_system_font found in globals: True
ConfigBase::get_item: ConfigBase::get_item: geometry_hinting found in globals: False
ConfigBase::get_item: ConfigBase::get_item: focus found in globals: click
ConfigBase::get_item: ConfigBase::get_item: focus found in globals: click