Thank you for your effort.
In my opinion your observation what's in the source code does not match the explanation given in the link (I believe the explanation is wrong/outdated, not the code 
).
- The source code suggests that all DNS queries are prefetched. This in line with what I see because a lot gets prefetched.
total.num.queries=5292
total.num.cachehits=4460
total.num.cachemiss=832
total.num.prefetch=2735
--> Disabling Pihole's cache is not necessary, prefetching happens anyway.
- The deeper explanation given in the link is in line with
unbound.conf manwhere 10% more traffic is expected as
If a client requests the dns lookup and the TTL of the cached hostname is going to expire in less than 10% of its TTL, unbound will (1st) return the ip of the host to the client and (2nd) pre-fetch the dns request from the remote dns server. This method has been shown to increase the amount of cached hits by local clients by 10% on average."
--> Disabling Pihole's cache might be beneficial as Unbound would be queried already for "close-to expiring" entries and not only for "already expired" entries
As I actually see 1) it leads me to the conclusion that the explanation given in 2) is wrong/outdated (they might have changed the behavior at some point).
Conclusion: Prefetching works also with Pihole's cache enabled and aside from a theoretical tiny tiny speed improvement there are no additional benefits from disabling it (but negative side effects on DNSSEC might occur)