Matrix is best at forcing it, it will likely charge out as multiple one-ways though as the routing likely violates maximum distance rules (hence the error), which (likely) will be more expensive.
Domestic fares don't have MPM rules, they have specific routing rules. But, yes, LAX-RDU fares do not permit JFK routings in routing rules (from EF below). You can still price LAX-JFK-RDU on single ticket as broken fares, but there can potentially be married segment inventory availability issues if connection is less than 4 hours (while not always the case, there can be times where it does not match inventory on individual flight segments and multi-city searches only look at individual segment inventory). Fare pricing must use the married inventory availability when purchasing the fares on a single ticket which is likely why you are seeing the price change message. You will likely not encounter message if pricing with a connection over 4 hours (as there is no married inventory maintained on such connections domestically).
MAP CONSTRUCTED LEFT TO RIGHT AND RIGHT TO LEFT
1. LAX-AUS/BNA/RDU-RDU
2. LAX-CHI-RDU
3. LAX-CLT/DFW/MIA-RDU
4. LAX-DFW/LAX/PHX-CLT/DFW/MIA-RDU
5. LAX-PHX-RDU
6. LAX-RDU