Your own examples show that the 'comparison word', as you call it, cannot be the determining factor. Consider the following two examples you provided:
My supply of apples has increased by 200%, to 300 apples.
(the original quantity excluded)
My supply of apples has increased to 200% of my original supply, so now I have 200 apples.
(the original quantity included)
Same 'comparison word' (the verb increase), different 'inclusion' properties. So, no, the 'comparison word' is not decisive. Note that in the case of the verb increase, in order to say anything quantitative about the amount of increase, we must use a preposition phrase (PP) complement.
Note that this has nothing especially to do with percentages. If I had 60 kg and gained 10 kg so that now I have 70 kg, I can describe that using either of the following:
My weight has increased by 10 kg.
My weight has increased to 70 kg.
All I can say is that the prepositions by and to work in this way (by having the 'exclusive' meaning, to having the inclusive one) with many other verbs besides increase. Some examples include swell, boost, expand, surge, rise and many others (and their antonyms like decrease, contract, decline, shrink, etc.).
With the noun increase, we have something similar. Say that initially there were 40,000 units, which the Ministry projects to increase by 10,000 units to 50,000 units total. We can say
The Ministry projects a 10,000-unit increase.
The Ministry projects an increase of 10,000 units.
The Ministry projects an increase to 50,000 units.
In the case of more, when it follows a quantity, it is determinative, in the sense that it is always interpreted as 'additional':
All I need is $5 more.
Your next-to-last example is indeed specific to percentages and fractions. Here the presence or absence of other words matters. For example,
If I have 150% of my original 100 apples, then I have 150 apples.
If I have an additional 150% of my original 100 apples, then I have 250 apples.
If I have a double of my original 100 apples, then I have 200 apples.
If I have an additional double of my original 100 apples, then I have 300 apples.