@John McKee, I have no direct experience with this scenario, but here are some thoughts:
First, drive thru's are limited to banks (and even these seem to be disappearing) and restaurants. Is this realistically a restaurant location? Is building over the drive through limiting your ability to punch a hole in a wall, re-stripe the traffic pattern and, and put in a restaurant drive thru, when/if the time comes?
Personally, I don't see a bank drive thru as valuable. Most banks are retracting their physical footprints, and when they are opening new locations, there is a drive through ATM, but not 2-3 lanes of drive thru teller access.
Broadly, I think the finished, leasable sq ft is more valuable. The challenge is going to be striking a deal with the tenant. Yes, they are paying for the new finished sq ft. But you are also foregoing the ability to finish that yourself and find a paying tenant for the space. One option is to "charge them" rent for the new sq ft at market rates. Then, provide a rent abatement for X yrs to offset their costs.
I.e. they expand the building by 2,000 sq ft. Market rent is $15/sf/yr. It costs them $200,000 to build the addition. You could straight line it and give them 6.5 yr rent abatement on a 10 yr extension.
Or, you could create a ground lease on the addition parcel and say the rent for that ground lease is $2,000/mo. But this could be overly complex when it comes to prorations for NNNs, since part of property is on GLA and other is on ground lease without being separately parceled.