Good question, I would not do a giant IF statement, but rather another boolean line item. So, Options is a list with a top member (All Options), and A through F is a list (Projects). Line items would be Valid (this is your boolean or what you currently have as an X), set the summary to Any.
In your SYS Projects module (the A through F), create a boolean line item named Valid Options? with the formula: Module.Valid where "module" is your matrix above. This will return any Project where Options are checked. This will effectively get you out of the nested IF statement.