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In most cases, the tradeoff of slower updates is worth it to me. For NewPipe I use their own repo to get faster updates, because YouTube breaks too often and I trust NewPipe not to include garbage. From the build metadata for NewPipe I can tell that F-Droid makes literally no changes to NewPipe on their end and does not use a custom flavor (as some apps often define) to build the apk, so I can reasonably trust that NewPipe by default follows F-Droid standards without any changes.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.