Electronics will be similar, so will the operational and maintenance procedures.
Gripen E is way better in range. And its airframe will also be better since it has canards while both aircraft have the same weight and engine power. The weapons layout design is also better and Gripen has better weapons options.
LCA will be easier to upgrade. The IAF is familiar with the design after the Mig-21 and M-2000 experience.
Although the LCA is cheaper, Gripen has a longer life. That more than compensates the difference. LCA Mk1 has a service life of 3000 hours and Mk1A may increase to 4000 hours. Mk2 could be higher. Whereas Gripen E has a service life of 8000 hours.
If I were a third party AF looking for air to air capability, I would choose the Gripen over LCA any day. But if the LCA carries the Kaveri engine, then all of Gripen's advantages become irrelevant. This engine will make any aircraft special.
If I were a third party AF looking for air to ground capability, then Gripen is the only option. Meaning, it is a better multirole aircraft than the LCA.