The clockspeed thing isn't so much as issue, as it is a harsh reality. Some of us have CPUs which are stable at 1.2GHz, and some of us don't. Somehow, the ICS installer is testing this during installation. No one has identified exactly how this is accomplished, but my guess is some sort of stability test based on something like prime number factorization. If it kicks out a bad result, the CPU is clocked at the lower speed. If the result is what is expected, it clocks itself at 1.2GHz.
As for the lapdock, i'm not even sure Moto/VZW even care, as the Bionic lapdock seems to be a thing of the past. My guess as to the root cause is that the lapdock's non-standard (for Android) 1366x768 resolution is somehow throwing off the launcher (which is probably coded to expect more standard resolutions such as 720p which is 1280x720). This would explain why it has no issues plugged directly into a 720p TV via HDMI. The reason switching to a different launcher is likely due to the fact that the non-stock launchers simply play nicer with nonstandard resolutions. Basically, Webtop 3.0 simply puts the launcher in "tablet mode" - and as far as I know, none of the tablets use a 1366x768 screen. Why Motorola didn't simply design the lapdock with a 720p screen is the question. Probably wasn't an issue with the old Webtop because that didn't use the stock launcher.
All of this is just speculation, but makes sense if you think about it. It would have been nice, however, if they had thought of Lapdock owners when designing the ICS launcher.