You are correct that this may change tonearm compliance and it is really meant for problematic tables. Plasticlay can be a friend or a foe if used incorrectly.
In the Audio Basics, as an example, clay was used to remove the rattle from a loose counterweight, or a shaking counterweight dial. I have some on my DIY turntable, called ARCom, as the counterweight had both of these problems and a small dot of plasticlay completely cured it. I also used plasticlay to affix an additional weight to the counterweight, as it was missing a part, allowing for use with heavier cartridges.
I have also experimented with clay on the shaft near the tonearm pivot, to remove some unwanted vibrations coming up the tonearm. There certainly is some trial and error when we start fooling around with the cartridge end of the tonearm. If you suspect the tonearm is transmitting unwanted vibrations and their harmonics, this method could help. However, care must be taken in proper placement and amount used as too much clay may steal energy away from the cartridge. I suggest very small dots to begin with in strategic locations.
In many cases, you may remove tomorrow, what you put on today, because the root cause was not found and incorrect applications may make matters worse.
Part of the problem lies with vintage tables, where parts have become worn or loose and plasticlay is certainly a great way to heal some of these problems.
And yes, any amount of clay you add to the arm will require rechecking and adjusting of VTF.
Wayner