Yeah, it's really not very meaningful, if you add something, that changes the reference (from "unlimited uses of the metamorphic ability" to "unlimited uses of it's supernatural ability").
You can deny that reference, if you want to, but it doesn't make it go away.
If you run towards a rock and close your eyes, you'll still bump into it.
Each time you change your form, such as through the metamorphosis power, you gain one of the new form's supernatural abilities, if it has any.
You gain only three uses of the metamorphic ability per day, even if the creature into which you metamorph has a higher limit on uses.
If you look up the references from back to front... the higher limit of uses refers to the uses of the metamorphic ability, which can only mean, that the metamorphic ability is the supernatural ability of the creature you metamorphed into. Now, this metamorphic ability can only be the new form's supernatural ability you gained from the first paragraph. This ability has a 3/day limit, as the second paragraph tells us. You gain one such ability each time you change form, as the first paragraph tells us, limit included, since the second paragraph refers to the first and the limit only applies to the supernatural ability you gained when metamorphing.
The following example, using 'ability' twice in the same sentence, once referencing the "metamorphic ability" and once the "supernatural ability" is further evidence, that those are the very same 'ability'.
For instance, if you gain a dragon's breath weapon, you can use that ability only three times before losing access to the ability for the day.
By the way...
What 'it'? There is no 'it' in the sentence... 'it' is left out, because 'it' is unnecessary, since the first part of the sentence already states 'it' ("metamorphic ability").
And again, your version of 'reading' it, is much more balanced (I probably still wouldn't allow it, even with that restriction applied, but it's
a lot closer), but it's simply not supported by the text, unless you completely deny what is written there and replace it or add stuff that's simply not there (which in turn leads to the restriction you are talking about).
Bye
Thanee