Answer in 2 words:
The location of Xserver for GDM is hard-coded at compile time in configure.ac, line 1199 in X_SERVER variable and can't be configured. So, may be you could play with symlinks, linking /usr/bin/Xorg (or, less probably /usr/bin/X, see this) to your build of Xserver.
Details:
I have a Debian 7, too and here's my process tree:
|-gdm3-+-gdm-simple-slav-+-Xorg
| | |-gdm-session-wor-+-gnome-session-+-bluetooth-apple---{bluetooth-apple}
| | | | |-evolution-alarm---2*[{evolution-alarm}]
| | | | |-gdu-notificatio
| | | | |-gnome-fallback----2*[{gnome-fallback-}]
| | | | |-gnome-panel-+-gnome-terminal-+-bash
| | | | | | |-bash---vi
| | | | | | |-bash-+-less
| | | | | | | `-pstree
| | | | | | |-gnome-pty-helpe
| | | | | | `-3*[{gnome-terminal}]
| | | | | |-iceweasel-+-plugin-containe-+-4*[gtk-gnash]
| | | | | | | `-{plugin-containe}
| | | | | | `-31*[{iceweasel}]
| | | | | |-pidgin
| | | | | `-3*[{gnome-panel}]
| | | | |-gnome-screensav---2*[{gnome-screensav}]
| | | | |-gnome-settings----2*[{gnome-settings-}]
| | | | |-gnome-sound-app---{gnome-sound-app}
| | | | |-metacity---3*[{metacity}]
| | | | |-nm-applet---{nm-applet}
| | | | |-notification-da---{notification-da}
| | | | |-polkit-gnome-au---{polkit-gnome-au}
| | | | |-ssh-agent
| | | | |-tracker-miner-f---2*[{tracker-miner-f}]
| | | | |-tracker-store---6*[{tracker-store}]
| | | | `-3*[{gnome-session}]
| | | `-2*[{gdm-session-wor}]
| | `-{gdm-simple-slav}
| `-{gdm3}
So, Xorg is started via gdm-simple-slave. Definitly, /etc/gdm/Init/Default has nothing to do with starting Xserver, as it was said here and here.
There were some indications, that it's impossible to configure, how X is started from gdm.
I decided to go for source codes, which are pretty well structured. So:
Go to the source codes, there is a daemon folder, which contains an INTERNALS file, explaining the structure of code.
There you can read:
** GdmServer
A class, used by the slave, that manages running a local X Server.
So, the file we need is https://git.gnome.org/browse/gdm/tree/daemon/gdm-server.c
There are several nested functions, responsible for calling X server and creating its command line arguments.
The function directly responsible for running X server process is gdm_server_spawn, which spawns the X in the line 694 with glib's g_spawn_async_with_pipes.
So, we're to find out, how its argv is formed. Well, in 2 words it's line 293 and we need the value of X_SERVER macro (unless you're using RedHat's systemd instead of sysVinit, but you aren't :)).
Alas, this macro is seemingly formed in configure.ac, line 1199 and is hard-coded. So, it seems that the best option is to place a symlink to your build of Xserver to one of those locations.