It's not how close it is to the PLL being far from the DDR2 pins. Even if it were right next to them, it still drives global/regional clock trees, which basically is driving to the middle of the clock tree and then fanning out in a balanced structure(probably H-tree).
The problem is that the PLL is not being driven by it's dedicated clock pin.
Note that altmemphy used a macro timing model, whereby hardware was actually evaluated to determine how much margin it had, then modeled for all the PVT variation, etc. Because of this, if you do something that is different than how the original setup was done, such as not using the dedicated clock driver, the results could be different. The problem with macro models is that we just don't know how much different it is.
How fast are you going? I have seen numerous designs with this issue, where the board is already laid out and there's not much they can do. In the end, everything works fine. The reason it's a critical warning is to try and bring it to your attention before the board is laid out. It's not an error though, since it can be done this way. In general you should be fine unless really pushing the boundaries of what it can do. (Sorry for not having a more yes/no answer...)