I know from studying and paddling commercially made boats, it's very rare that you need a fully extended skeg. Maybe for surfing but that's about it.
If you have a skeg that is longer, you will not loose too much speed if you just crack it an inch or less to stiffen up tracking. If you have a skeg that needs to be lowered down deep to work well, you will feel the loss in speed noticeably. A lot of commercial ones are about 10" or longer. The ability of the skeg to work is dependent on it's length much more so than how far it is lowered.