First, with all your examples, it seems that allowing ANY quantity to be entered in Quick-Add is not a good idea. If what you say is true and there's no way to audit it, why would you want to allow ANY manipulation of quantity in there?
Besides that, though - and to wander from the software itself for a moment - I think it's easy to go too far down that path of agonizing over employee dishonesty. I really don't think any business is ever going to be able to plug up every possible form of employee theft, and I don't think any piece of software is going to prevent it if a person is determined and has any sort of computer skills. I've worked with inventory-related software with perpetual inventories for 20-25 years now, and have yet to see one where inventory does not have to be corrected from time to time for reasons not related to pilferage.
I had my business going for 2-3 years before I brought in employees, and I had one hell of a time adjusting to having to trust someone else. I eventually decided that I either had to trust them implicitly or get rid of them. And I continue to watch for signs of anything under-handed going on, but I'd have been forced by ulcers or something years ago if I focused on every last bit of minutiae.
I try to reward my employees generously - partially to enhance their "buy-in" to want the business to so well, but also to keep them from feeling the urge to "even up" by resorting to something like theft. I feel that this approach has done well for me, as I'm celebrating my 10th year in business this year with both sales and profits continuing to improve substantially.
But yeah, maybe "quantity" should not be allowed to be entered in Quick-Add.