Basically only the items that are in Box 1 of the W-2 are compensation.
What you have termed office advances are likely distributions that are not wages or salary so are not here in officer compensation but rather are part of the distributions listed on Schedule K line 16d.
The unallowed one half of business meals is not compensation but is nondeductible expense of the corporation. This may be on Schedule M-1 if required, otherwise is only on the corporate books.
It is a requirement that an officer providing services to the corporation take a "reasonable salary" so the most correct treatment is to file a late W-2 if the officer did take money from the corporation and did provide services.
"Distributions and other payments by an S corporation to a corporate officer must be treated as wages to the extent the amounts are reasonable compensation for the service rendered to the corporation."
This is a legal requirement and not a matter of choice or convenience.
That is, there is no other correct manner to report officer compensation of a more than 2% owner of an S corporation other than in Box 1 of Form W-2 when the officer has taken money from the corporation and provided services. .
If there were personal, not business, meals or other expenses paid by the corporation for the officer those will should also be part of the compensation in Box 1 W-2 but might be treated as distributions on Schedule K.
There is no need to file or include on Form W-2 money taken that can property be designated a loan which will be repaid. Even the personal items paid by the corporation may also be a loan to the officer. This is a part of the balance sheet.
The W-2 total from the payroll service is the correct amount to use in line 7 of Form 1120S (unless you choose to leave it in the payroll services total as previously discussed) and the other amounts will be on Schedule K as distributions. Health insurance paid and other benefits are already part of that Box 1 amount when done properly, or you may need to consider a corrected W-2 .
Hope this clarifies for you (even if not what you wanted to hear).
Please do ask if you need more help.