To protect against warranty issues for some systems. I never really saw a reason for one.
CMP instructs they be used with their system. As the installer, I have to follow them or I accept the liability. A warranty service comes out, inspects the installation, denies the claim if not done according to the manual. It happens.
From the manual:
2. INSTALLATION LOCATION
a. It is recommended to install the salt cell installed as the last piece of pool equipment in line, on the return to the pool,after the heater. (See illustration 1 on next page)
b. Installing horizontally will ensure the flow sensor remains submerged.
c. If installed vertically, the cell cap must be on top.
d. Always use a check valve before the cell to prevent chlorine backflow.
e. All fittings are 2 inch Socket.
f. NONE: Do not install on pools using a stainless steel liner or stainless steel plumbing.