I'd seek advice from someone well qualified in planning matters. So long as all details of your development to the rear are compliant with the exempted development regulations, you are entitled to build that. Doing so before the proposed extension to the front means you have the full 40sqm to play with. The 40sqm exemption applies to the original footprint of the house, so the area any other extension work comes off that total.
Where it gets complicated is in applying for permission while also carrying out exempted development. You'll need to supply site plans, I'm not sure how likely a site visit is, but if they see an extension going up that wasn't on those plans...
So long as you meet all other criteria for exempted development for the portion to the rear, could you not include that in the planning application? That would greatly simplify the process if you ever go to sell the house.