No, the Swiss Travel Pass Flex is not offering any advantages on the days on which it is not activated. Your assumption was right in the past, but it was changed a few years ago. Today, you can only use it on the activated days. The advantage of the Swiss Travel Pass Flex is nowadays that you can choose on what days it is valid and only pay for these days. So to speak, you pay for the flexibility.
However, personally, I think, the Swiss Travel Pass Flex is not very useful, and I must say, working as a ticket inspector, among all Swiss Travel System products, I do rarely see the Swiss Travel Pass Flex.
Had you asked me for the best ticket, I would have suggested the Swiss Half Fare Card plus single tickets or in combination with Saver Day Passes. Both give you the same flexibility as the Swiss Travel Pass Flex.
Swiss Half Fare Card – Switzerland at half the price | SBB
Saver Day Pass – book earlier, travel cheaper | SBB