Post your SAP so we can take a look. I’m very surprised that a timber frame is failing the SAP.
I would also assume that the junction calculations are taken from standard details rather than specific construction drawings.
The condensate collection pipe should be insulated inside and outside the unheated space and should terminate to a suitable foul drain - not a rainwater downpipe. Failing this it can be connected to a limestone filled sump > 1.0m from the foundations.
If the boiler is inside an attached garage/space a CO detector/alarm should be fitted.
Also you may need to have a Building Control Application made for the works.