Just wanted to chime in to share my experience, doing the same hack on the CM3 as a result of the same TE connector, in case it's helpful to anyone. More details here of my solution viewtopic.php?f=98&t=190048
I modded a pi module the same way, by cutting the key notch just slightly (with a dremel) to allow for placement of the pi module in the DDR (vs DDR2) connector. I then powered up the system and it booted great and I thought all was great, but then I started having problems with booting. Some power ups would boot fine, and others (more than half the time) would not boot up at all, nothing over the serial at all. So apparently I must have slightly dinged an important internal layer trace (or two) from my cutting, to cause the booting (and who knows what else) to become unreliable. For a short term proto hack and more careful notch trimming, this still might make the readily available DDR TE connector work ok-ish, but it's not a production solution, which is probably the use case for a lot of compute module users/integrators.
The other risk of trimming the key notch approach, is even if it doesn't damage any internal layer traces, it now means that the module contacts don't align automatically with the connector pins. With them being only 0.6mm pitch, it doesn't take much side to side sliding for them to not align correctly.
Anyway, my solution (thanks to another's generous sharing) was to find this correct DDR2 connector from JST: http://www.jst-mfg.com/product/detail_e.php?series=520
. Unfortunately, it wasn't readily in stock from Digikey, but I was still able to get some samples from JST and now it's working.