The whole concept of fungible contracts is that in the proper ratio long and short positions net out to a zero position during the daily settlement process. The CBOT literature on Dow Futures clearly specifies this: Fungibility CBOT mini-sized Dow ($5 multiplier) and CBOT DJIA futures ($10 multiplier) are fully fungible contracts. Fungibility allows the offset and liquidation of CBOT minisized Dow against CBOT DJIA futures held in the same account, contract month, and year in a ratio of 2 to 1. Are you telling us that IB can't properly handle a simple fungible contracts offset during the settlement process?
I understand that "Fungibility is not mandatory", but if I want to use the fungibility of YM and DJ or ES and SP can IB perform the offset during the clearing process? CME and CBOT members trading pit contracts against fungible electronic contracts use the fungible contracts offset every day. Hedging a position with a fungible contract is not a true hedge, it is an offset. A true hedge requires two similar, but nonfungible contracts.