Yes, I had the same question some time ago.
But, here in Italy, it will not be a real issue, because an experimental airplane, when using a certified engine (which I had to buy), can be approved for IFR use, but ONLY in VMC conditions. It is forbidden to have an experimental airplane flying into IMC conditions.
So, as far I understood, there is a bit of non-written tolerance from ENAC engineers (equivalent to FAA) about mixing together certified and non certified stuff and about strict compliance to rules which apply to the actual general aviation airplanes (for instance, I was not asked to install an ADF, which I installed, however).