If anyone missed it, I believe what the OP is refering to is that the booking system requires that segments be in the same fare class. So, all segments of your outgoing trip has to be in L for example... they can't be mixed T + L. It allows the outgoing and return portions to be different as long as the connecting segments for the respective travel day are the same.
Now, the issue I've had is this can cause some strange problem when trying to book with the reserve first class companion cert. That one allows you to book in A... however if one of the segments is on a RJ with no F cabin then it appears to only work if there is L available on that flight.