Calum, your description of the penetrant crack detection process is good. I used to be the one checking rolls prior to installation in a steel mill. I used a penetrant kit to test for cracks in the drive tang end. It was a relatively well machined area in bare metal. The method will only detect cracks of a "reasonable" size and the "seed" cracks just starting may not be found. I took photos of the " developed" test area to cover my arse!
The idea solution for the M3W chassis would be to reweld the joints in the affected and nearby areas adding the strengthening fillets at the same time. Remember, afailed joint can result in a neighbouring joint being affected. No compromise with poor welds by visual inspection tolerated. The coatings on the chassis should be removed completely by a non aggressive method...chemical preferably to prevent peening/ deformation that hides cracks. Perhaps a full replacement of chassis? This would allow the old one to be thoroughly checked and then " rebuilt" as a replacement? I do not have a M3W so cannot comment on the feasability of access to check/ weld as an upgrade so apologies if I am oversimplifying things.