EDIT: Also, the fact that people can even say that the genius who worked on his computer purposely left the dent there - if they even caused it in the first place - and did absolutely nothing about it hoping that the OP wouldn't notice it is an insult to his work. I find extremely insulting, and I don't even work for the company anymore!
I agree, unless their extremely clumsy (in which case they will get found out eventually) I'm sure Apple would much rather they owned up to making a mistake and replaced the part.
However, clearly people can be dicks, both the customer and some Apple staff. I recently had an experience which highlighted this.
My wifes 2009 MBP suffered an expanded battery for the second time, after only 300 cycles on the replaced battery. I took it into the store I purchased from, and the manager incorrectly stated since it had already been replaced once my consumer rights didn't apply. Worse still he refused to remove the battery to confirm it was safe, stating it "probably" was. Apparently they tend to expand some more when the case is removed and he insisted they wouldn't return the machine sans battery and therefore only open it if I agreed to pay for a new one. He kept asserting I'd already had a "free" battery, when what I'd actually had was a replacement for a defective battery (which I'd paid for as I didn't get the machine for free).
Obviously I wasn't happy with this, as it had two premature battery failures, I wasn't paying for another one given this history. And I certainly wasn't opening it to examine the battery and replace with OEM, once they'd told me it usually expands some more when you open the case. Given my field of work, I've been conditioned to treat lithium polymer batteries with care particularly when they've started to lose physical integrity.
I took the machine back, explained my concerns to Apple Care, who agreed a replacement part did not preclude my consumer rights. They booked me into another Apple store. Some quick tests later, which showed the battery was still reporting as healthy, they agreed to replace it. Far more in line with the experience I'd expected. NB I didn't necessarily expect a free battery, if they'd shown it had depleted naturally I would have been happy for them to remove it. Both he and Apple Care agreed this was a reasonable position, as while the battery was probably safe, I had a right to be concerned given the potential results had it not been safe.
I left it with them for 5 days, as I was going abroad and he wanted to inspect the machine to see if there was a root cause for the two battery failures. When I returned to pick it up I noticed he'd incorrectly logged it had a scratch on the Apple logo instead of on the top case. It did have a scratch on the top case which he hadn't logged (I'd once rested it ontop of its sleeve at airport X-ray. Unfortunately after I passed through the scanner, the idiot attendant must have put it, in its own tray, but top down

).
Now had I been unscrupulous I could have claimed they'd caused this scratch, as it wasn't logged. Given how busy the store was, the Genius wasn't going to remember his mistake and they would have had little choice but to accept my assertion. But I try to live by the moto what goes around comes around, so just pointed out they'd made a mistake and the scratch was pre-existing. I really didn't feel like taking advantage of a minor slip up, during a very busy time in the store (teachers strike was on, so lots of people had free time to pop in with their kids), despite my experience with the previous store manager. But I'm sure many customers would have grabbed a free top clam shell at Apples cost

and its behaviour like that which leads to manufacturers having to be less generous and trusting

.
If they handed out replacement machines in these circumstances, it simply leads to moral hazard and more customers behaving badly IMO. Having had experience with other retailers/manufacturers IMO the OP's resolution is fine. It will be logged that they dented the machine and the OP can use this to his advantage in the future, should they refuse a claim based on physical damage. But equally theres enough inconvenience (as opposed to simply handing out a new machine) to deter those being unscrupulous.