Dumb analysis that entirely ignores the ISEs.
First educate yourself what Indian specific enhancements are, before you make inaccurate claims and make up cost advantages!
Mirage 2000 Upgraded to FOC: Yet Another HAL Project Takes-off on Schedule
...The FOC configuration covers the integration of Indian specific weapons, sensors and EW system. This FOC upgrade on Mirage 2000 gives additional capability of air to ground weapon, training, helmet mounted display etc...
http://www.hal-india.com/Mirage 2000 Upgraded to FOC Yet Another HAL Project Takes-off on Schedule/ND__172
Indian specific enhancements, are capability corrections or upgrades, to make a fighter suitable to IAFs operational requirements. They are applied to all fighter procurements or also upgrades as you can see with the commonality of the Mirage 2000 upgrade and Rafale enhancements, but also to MKI or Mig, Jaguar upgrades.
They are also requested by IAF and not negotiated by a specific party, therefore is not something special to the Rafale deal.
Rafale did not had HMS, nor a capable targeting pod, that's why 2 of the enhancements / capability corrections, were the integration of Israeli systems to counter these shortfalls.
The EF had HMS and the Litenting pod integrated, so would not have needed these corrections and therefore no need of these additional costs. The rumored thrust enhancement for M88 engines is another capability correction, that comes at extra cost, which again would not be needed for the EF, with the highest TWR of all MMRCAs.
Even if you compare it to Gripen E, the Rafale is in disadvantage, since it not only gets 2 different HMS options, but also Litenting LDP and via Brazil even Spice integrated. So all these costs can be avoided, while they were necessary for Rafale!
Not only the flyaway unit cost is likely to be lower, but also the cost for Indian specific enhancements, while the operational costs advantage of an SE can't be matched by Rafale at all.
Your notion that Rafale wouldn't need infrastructure costs is also illogical, because we only paid for 2 bases. The new MMRCA tender however is for new bases in different areas of the country, so even if we order more Rafales, we also have to pay for new infrastructure.
Rafale is and advanced fighter, with a lot of good capabilities, but they come at a high cost. IAF is clear that they want to make up numbers and that's not possible with a costly Rafale and the low defence budgets. That's why they wanted the SE MMRCA route and sInce the SE contenders are also still in the tender, will have the cost advantage.