If you come back and It is not noticed and no interview required probably nothing will happen. Get visa and go on Visa run to activate it. However, why even start the application if you need to return to Thailand urgently - why not fly today?
When the WP is cancelled the B need to be too. Employer cancels WP then employee must go to Immigration and cancel B. The B is tied to the WP and is invalid when WP cancelled. Normally have 7 days to leave Thailand ie can do visa run. He can go to Immigration Monday.
The 90 days is 90 days. The weeks leeway is if you actually report. Currently there is no issue leaving or re-entering if you do not complete the 90 day report. However, it is a requirement for your visa and immigration always have this recorded. Some "O" Visa holders do not report and pay a fine once a year when renewing their visa. As the Thais say "Alai gadai" (Up to you).