This is a terrible design choice and has effectively ruled out the Minima for use with the onboard RTC. Also tying the VBATT pin to +5v has made it hard to do a mod to access the pin as well. The only option I can see is to use an external RTC, which is such a waste.
You, are totally right.
I don't understand this design either.
On the Uno R4 Wifi the VBAT is connected to an external pin.
Why not on the UNO R4 Minima?
That's because there's no external 32.768kHz crystal on the board. Instead the R4 uses the RA4M1's much less accurate, 32kHz-ish, low speed on-chip LOCO oscillator.