I have some recent experience of this though ORK-BOS.

MFU ex Ireland with EI codeshare to LHR have to be booked via call centre. Sadly, this can lead to some unwelcome surprises with the final total.

As a quick and recent example:

Travelling in early september WT+ return (planning MFU to CW rtn):
ORK-BOS about 50 euro in the difference over the WT+ return fare ex LHR. Did a dummy booking for flight choices LHR-BOS - no problem with MFU usual 25000 miles etc. Proceed to call up to attempt to book ORK-BOS with MFU on the LHR-BOS leg. Bottom line could be done, however the base fare went from about 800 euro to 2200 euro + miles. Much discussion about this with pleasant agent lead to perplexing explanation of fare rules.

Solution
1. book ex LHR
2. deal with EI directly for the connections (90euro)

3. or pay an extra 1300 euro to have it under one booking

Will be interested to hear what happens.