I have heard before that a light flimsy transport is not as good(causes jitter) as a heavy damped one. And I have also seen modifications that add weight or damp parts of the transport or player.
How exactly would physical vibration affect the jitter or clock or the sound for the matter of fact ?

Certain electronic components (well, theoretically, all of them) are microphonic. ie, vibrations are transduced into electrical phenomena. This can in theory inject noise into the system, which while small and would not affect the digital data, would affect the data timing.

In reality the microphonics for discrete components and most cables are phenomenally small and possibly unmeasurable. Especially for vibrations as small as those coming from a CD motor. Vacuum tubes, in contrast, have extremely large microphonics. You really need to look at the numbers, and the audibility from a blind-testing standpoint, to judge if such tweaks make any sense.

EDIT: And you can ignore jitter entirely if you're talking about CD-ROM drives that read their data through bus interfaces rather than analog or SPDIF. Those are completely immune.