At any airport that I have operated into that has this potential problem it is normally covered by an explanatory note, along the lines ".......min flap retraction is 1860' AAL.....".
We were also told that when we saw these non standard MFRA's the RTOW had been adjusted/decreased accordingly to make the second segment climb.
It was also useful to be wary of the MFRA in the event of a missed approach if the runway was also a landing runway. (Again assuming the normal climb gradient in the event of a GA)