What you saw in that EK9 swap photo is what it's going to cost to purchase an EK9 to swap into the older Civic, which is done from GT Auto instead of the Tuning Garage. Assuming that is the final price, that will represent a 100,000-Cr. premium over what it would cost to replace the EK9 in the Tuning Garage, whether it was in the newer Civic or the older one.
In the case of the Supra-to-Yaris swap, to make the swap should be 210,000 Cr., but don't hold me to that. Once the swap is made, replacing the engine via the Tuning Garage should still be 110,000 Cr.
Late edit - Memo to self - check the swap prices of the 1998 Civic and 1965 Mini as those two cars are of different parts price tiers, but share the same engine swap, as well as whether the Supra engine swap has a different price premium than the 2020 Civic swap as those two donor cars are of different parts price tiers.
Not to mention that the prices of the swaps from cars that are in Hagerty's will (likely) change when the price of the donor car changes.