If the MOD are genuinely using Bowtie type methodologies without a proper numeric or quantified assessment they are being deliberately casual and legally non-compliant (suitable and sufficient risk assessment!).
I've closely followed DV's excellent work on this accident and made a number of observations.
1. Numerical risk assessments were outlawed by the CAA in the early 90s and MoD immediately fell in to line. They have never explained why they have (apparently) changed back. It must be very confusing to those FEW in MoD who actually do Risk Management.
2. Throughout the 90s and 00s, MoD's stated policy on Risk Management was - "Wait to see if the Risk materialises, then do something". In furtherance of this poilcy, programmes were denied the mandated resources to appoint a Risk Manager. The inevitable happened - MoD lost its corporate knowledge. (Read the Wg Cdr Spry thread!) When something happened, it often involved loss of life. Accidents that fall in to this category include Sea King ASaC, Tornado/Patriot, Nimrod, C130, Chinook and this one under discussion. That is, the Cause(s) and Contributory Factors were all known and notified years in advance, and conscious decisions made to wait to see if they materialised.
3. Allied to this, and your own comment, in this period MoD policy was to ignore altogether the concept of trend failures and the need to apply mitigation to the WHOLE fleet. In particular, Adam Ingram when Min(AF) stated a number of times in the mid-00s that it was completely irrelevant if a serious safety fault was known to exist in one tail number; that could not be used as evidence of the POSSIBILITY of the same fault existing in any other in the same fleet. This was utterly deranged but a natural progression from the Chief Engineer's policy of 1991 to cease all trend failure analysis, as part of his policy of running down the management of airworthiness.
There are exceptions to the above, but only because some decided to ignore these policies. In April 2005 MoD claimed in a briefing to PUS that, as of September 2004, none were left in MoD; but I'd disagree. Perhaps a handful do. It is those few who aircrew rely upon. Everyone needs to understand that for well over 20 years they have been the subject of outright hatred from senior staffs.
But latterly, in particular this last year and coinciding with the appointment of the new CAS, it has been very noticeable that MoD's approach has changed, at long last. Why? It is tempting to speculate he has read the evidence withheld from him in 1994. And to address your point; their answers in this case may claim they use Bowtie, but the detail they contain reveals many don't understand it or find it difficult articulating an answer when they know fine well the rules they operate under are so contradictory. The above explains why.