Here's an idea:
Disable buttons*(suggestion below).
Start at 50%.
No negative/positive modifier.
Once 0% reached, buttons reactivate.
How to disable buttons without disabling buttons? (love that sentence)
Give a colonized province a modifier: [Not fully populated].
While a province has [Not fully populated], if the decrease autonomy button is pressed, add 25% autonomy and a -10 unrest modifier for 30 years to the province.
While a province has [Not fully populated], if the increase autonomy button is pressed, remove 25% autonomy and add a +10 unrest modifier for 30 years to the province.
While a province has [Not fully populated], if LA reaches 0, remove [Not fully populated].
(This method should obviously only be a workaround until you can just disable/enable the buttons at will)
This basically disables the button until LA reaches 0, by going zero-sum with the modifiers.
This might be a more desirable way behavior for colonies.
Personally, I do like the current implementation. 100 years seems reasonable to me, keeping in mind that I start with a non-powerhouse nation to begin with. That it will be easier later on makes perfect sense. If you keep current implementation, I think it is acceptable to bump the <5 province bonus a bit. Perhaps to -0.20, to put it on-par with colonial nations government form.