Think of it this way...
I invest €100k in a non-BES/EIIS investment and it goes belly-up. I have a tax asset worth €33k (i.e. the loss) so my net cost could be €67k.
You invest €100k in a BES/EIIS investment and it goes belly-up. It ends up costing you €60k because of the income tax relief. Allowing the loss for CGT purposes really would be gilding the lily.