In almost every case you're correct. If its a hobby project, or it allows you to make a normal living you're likely to be fine. The danger comes when you end up founding the next facebook and there is some real money involved. Then you might have the Winklevii suing you based on the clause in the contract.
They could get expert testimony about the amount of time it took to create, find old stack exchange questions let alone get court ordered access to git etc. They may not end up winning, but you could settle just to avoid the cost.
On the other hand, this definitely counts as "nice problem to have" and probably isn't worth actually worrying about.
They could guess that I didn't create it in the last two weeks, but then good luck proving it in court.
I have much better relationship with my employer now, If I hadn't I would quit tomorrow.