"The difference between $6750 and $4500 was because the client sent me his 2020 5498 and not his 2021."

Either way, this is not a Tax Form. It would be needed, for instance, as reference for FMV in some scenarios. Think of it as Proof of Deposit. Not proof of tax treatment.

"Based on all this information, it appears that this is an employer sponsored plan and the $4500 was a pre-tax contribution and it "manifests" in his return in the form of lower reported gross pay."

It's already taken into consideration for the W2 values. You just enter the W2 as is.

"The explanation on H&R Block's site says that the amount listed in Box 12 with an "s" code was "not included in box 1".

You bought a program that knows how to handle W2 entries, as long as you use the proper codes for the specific boxes.