Yes, the first case charges more money, compare to the second case.
As stated in the doc you refer to (i.e. https://firebase.google.com/docs/firestore/pricing#operations):
When you listen to the results of a query, you are charged for a read
each time a document in the result set is added or updated. You are
also charged for a read when a document is removed from the result set
because the document has changed. (In contrast, when a document is
deleted, you are not charged for a read.)
Since your result set is smaller in the second case (because you use limit()) you are going to have less documents added to the result set.
For the case of Cloud Functions reading data of Firestore, if the region of your Cloud Function is not the same than the one of your Firestore (and is not in the same multi-region), you will pay for the Egress between regions. See, again, the doc you refer to as well as https://firebase.google.com/docs/functions/locations#selecting_regions_for_firestore_and_storage
Update, from the comments below
For the connection between the Cloud Functions and Firestore:
Egress within a region -> free, Egress between regions in the same multi-region -> free, Egress between regions (NOT in the same multi-region) -> not free, prices different if US or not US. See the table at the bottom of https://firebase.google.com/docs/functions/locations#selecting_regions_for_firestore_and_storage for details on the respective regions
Note also that, for Firestore, for the moment, the only available multi-region location is us-central, see https://firebase.google.com/docs/firestore/locations