For a milder hybrid, sandwich the electric motor between the engine and transmission or somewhere between the transmission and rear diff. And the batteries in that setup would be behind the seats and/or in an area below the soft top (when in the down position).

This first option has the benefit of being able to work with both manual and automatic transmissions.

For a ‘full’ hybrid, have a bigger electric motor integrated with the rear diff, get rid of the drive shaft and put the batteries where the drive shaft would normally be. Replace the transmission with an electric motor-generator. Also run the electric cable from the generator to the rear electric motor through the same area as the batteries are.

This option would likely have better MPGs and be eligible for more incentives. The downside... no manual.

And for a proper battery-electric car, a new BEV platform is required. Trying to turn the current MX-5 into a BEV is a waste of time with too many compromises.