My understanding, based on correspondance between me, First Capital Connect and TfL many years ago, is that a journey cannot begin or end with a Fixed Link - ie a Fixed Link must be sandwiched between two National Rail legs. This is why not all tube station have fixed links defined - only those that you can interchange at when using the Maltese Cross on the ticket to cross London (see National Rail's "Crossing London" page).
When you combine an Oyster tube journey with a non-Oyster National Rail journey, or buy a National Rail ticket to Zone U***, the tube isn't used to bridge the gap in the middle of a through NR ticket. Instead it's a National Rail journey and a tube journey tacked onto each other. I believe that in that case, the time you must allow for the tube part in this case is as defined in TfL's timetables and conditions, not in National Rail's Fixed Links. The documentation of how Zone U and boundary zone tickets work is sadly lacking, but I'd like to think that if there were no delays known about when a through ticket to Zone U** was bought, one of the operators would be liable to help if the connection was missed.