It seems that sometimes replacement buses are being used even though a through route would actually be available for diversion, because it's more operationally convenient for the TOC.
E.g. this coming Sunday, the Chiltern line is shut Wembley-West Ruislip, but rather than diverting Marylebone-Birmingham trains via Aylesbury and maintaining a through service (as happened regularly in the past), Chiltern are instead bussing Marylebone passengers between Bicester North/Village and Aylesbury.
The excuse they gave in response to my e-mail complaint is that although the rest of the route is open and the Oxford service is still running between Bicester Village and West Ruislip, they can't resource through Marylebone-Aylesbury-Princes Risborough-Bicester N-Birmingham trains because they can't access Wembley Depot and the other depots can't cope
From their response:
Whilst we do have access to facilities north of London Marylebone, these are small in comparison and the use of these for a full day service would add considerable pressure on to these facilities and because of this the planning team have faced some operational challenges when composing this amended timetable.
Personally, I think this is a bit of a cop-out, given that there are plenty of other stabling options and it's only a one day closure.