Currently, the mempool's minReasonableRelayFee is set to a hard coded value of 1000 (satoshis). (updated: https://github.com/bitcoin/bitcoin/blob/7f72568e6b15fc139323fb200591a50762f6df0b/src/validation.h#L54)
This means all results from GetMinFee are based on this hard-coded value, instead of the nodes set -minrelaytxfee, even if it is higher.
I think, at the least, if this isn't considered a network agreed basis for fee estimation, that mempool acceptance should be based on the nodes -minrelaytxfee instead/aswell.
Relevant code: https://github.com/bitcoin/bitcoin/blob/849a7e645323062878604589df97a1cd75517eb1/src/main.cpp#L907-L919
To verify, set -minrelaytxfee to anything, estimatefee 1 will be unchanged (as is also clear from the implementation)