I haven’t come across Guruji explaining this particular issue, but I can venture a guess.

The answer can be found in the Pañcopacāra pūjā. In the pūjā each offering is prefixed by a bījā (laṃ, haṃ, yaṃ, raṃ, vaṃ) representing a particular element which is connected to a respective cakra.

The final offering (which is related to Ājñā cakra) has a bījā saṃ, which is most often followed by sarvātmane or sarvatattvātmikāyai sarvopacāra pūjāṁ samarpayāmi.

“S” in bījā “Saṃ” is most likely connected to the word “sarva” meaning "all". It tells us that the final offering joins all the elements and embodies all the principles.