There turn out to be some annoying side-effects of disabling xkbcomp.
The problems I was were that the alt key didn't work in xterm or when
switching virtual terminals using crtl-alt-F1 (see bug #111372).

I have a little more data on how xkbcomp is invoked.  By changing
/usr/bin/xkbcomp into a shell script I was able to determine that during
login it is run 3 times.

1.         
|-gdm(14821)---gdm(14822)---Xorg(14863)---sh(9127)---xkbcomp(9128)---xkbcomp(9129)---pstree(9131)
    Called with args: -w 1 -R/usr/share/X11/xkb -xkm - -em1 The XKEYBOARD 
keymap com
piler (xkbcomp) reports: -emp >  -eml Errors from xkbcomp are not fatal to the X
 server /var/lib/xkb/server-0.xkm

2.        |-gdm(14821)---gdm(14822)-+-Xorg(14863)
        |                         
`-Xsession(9233)---xkbcomp(9251)---xkbcomp(9252)---pstree(9254)
Called with args: /home/ota/.keymap.xkb :0

3.        |-gdm(14821)---gdm(14822)-+-Xorg(14863)
        |                         `-sh(9233)-+-ssh-agent(9293)
        |                                    
|-xfce4-session(9338)---xfce-mcs-manage(9341)---xkbcomp(9342)---xkbcomp(9343)---pstree+
        |                                    `-xscreensaver(9304)
Called with args: -I -I/etc/X11/xkb -xkm /tmp/fileCbGof2 /tmp/fileaVT6TK

The second of these is due to my ~/.xprofile invoking xkbcomp "by hand".

Reviewing Oliver's strace output, it seems that xfce-mcs-manager reads
the output of xkbcomp (step 3 above) and sends it to the X server.

** Also affects: xfce-mcs-manager (Ubuntu)
   Importance: Undecided
       Status: Unconfirmed

-- 
xfce4-session seems to reset xmodmap
https://bugs.launchpad.net/bugs/97175
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