This is a very technical area, and your accountant would be expected to be good at at - that's why you are paying him. I think your accountant is correct.
The basis of any claim is against the proportion of the residential property that is used wholly for business purposes, and the HMRC guidance in this area is considerable and starts at BIM47815 here:
http://www.hmrc.gov.uk/manuals/bimmanual/bim47815.htm
From there, you might want to read BIM47825 (which gives examples using scenarios), and there are other pages that you may wish to look at.
Quoting 29% claimable of the internal work is a very precise figure, and my guess is that your accountant knows the proportion of your converted garage as a percentage of your total floor area in arriving at it.
If, once you have read around my links, you still have questions, I suggest you ask your accountant. I suspect he he knows something that I also know - you have to be careful with making claims for business use of a residential property or HMRC, when you eventually sell the property, will sting you for liability to Capital Gains Tax. This comes about because, although your Principal Private Residence is except from CGT, a partial use of your PPR for business can be treated as a commercial capital gain.
I suspect your accountant knows that claiming for capital repairs may throw you into this issue.
Alternatively you could take Ummm's advice. Clearly a lady who knows a lot about these things.