To the best of my knowledge there's no safety-related reason that you couldn't use a longer COL, provided of course that the round will still chamber properly and will still function through the magazine, which is usually the limiting factor with semi-autos. Also, with the bullet seated out further there will be less friction between the bullet and brass, which in theory could lead to problems with heavily recoiling calibers (the bullet can move in the case, or even come out of the case, under recoil).
You want to be sure that the bullet is not out so far that it's being mashed into the rifling (unlikely due to the magazine limitation, but possible I guess), which will lead to increased peak pressure. If you chamber a dummy round at the COL you want to use and then carefully extract it you should be able to see the marks of the lands on the bullet if that's occurring.
With regard to accuracy, most firearms have greater accuracy when the bullet "jump" is minimized, i.e., when the ogive of the bullet is just touching the lands. I doubt that it makes enough difference for pistol shooters to care, but it's important for careful rifle reloading.
There is also a very poorly understood phenomenon called "detonation" that allegedly can result with small charges of slow-burning powders and is said to cause extreme pressure excursions. That's why you see "minimum" as well as "maximum" loads listed for some powder/caliber combinations. It may be related to the large amount of extra space in the case, and increasing COL would also increase the space. My understanding is that it's primarily a potential problem for rifle cartridges and some magnum revolver cartridges, however. Pistol cases are comparatively small and most pistol powders are not slow-burning, of course, so I doubt that's anything you need to worry about with the cartridges you're loading.