Hello Artyum,
The CAP pin from the MPL3115 is the internal regulator output capacitor connection and therefore, the ‘second’ 100 nF capacitor should be place there in order to guarantee the stability of the internal regulator; but it does not mean that the internal regulator will be disabled.
Both the input VCC should use bypassing caps and the regulator 'cap' pin must have cap placed to ground.
As a reference, you can refer to the following connection:
I hope this information will be useful for you.
If I misunderstood your question, feel free to let me know. I will be glad to help.
Have a great day.
David Diaz.
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