I also doubt that there are miners who changes the default minrelaytxfee line to bitcoin.conf.
There are Bitcoin nodes do customization for their node configurations, but challenge for you is, you don't know where are these nodes and their IP addresses.
They can customize their node configuration like this.
https://jlopp.github.io/bitcoin-core-config-generator/They can customize this parameter
Min Transaction Relay Fee
Fee rates (in BTC/kB) smaller than this are considered zero fee for relaying, mining and transaction creation.
Probably meaningless if the propagation is poor, ie. if majority of the network doesn’t lower their mintxrelayfee Miners probably has a custom implementation of a Bitcoin node so it wouldn’t be out of the realm of possibility that they would include these in their mempool (miners regularly mine nonstandard transactions anyways).
I’m inclined to think that certain miners would operate in this manner. However, its probably difficult to tell given that mempools are often filled with txes paying above the minrelayfee.