Hello Francis,
The information attached to the D.cert application form reads, in part, 'Third party reference numbers are not applicable, ie www.ManxBMD.com etc', and I took this to mean only those references generated by Civil Registry are acceptable. Burial Register references would then be excluded (assuming they are not simply transferred to D.Certs). I'm afraid that I do not understand the reference to the 1911 parish register transcription - unless you're pointing out that it is more uptodate than Lawson? Whatever, the CD seems a useful tool so I'll send for a copy (this is the first I've heard of it - the IoMFHS site is neatly presented but lacking content; at the very least it should list the items it has for sale).
Regards and thanks
Alan