1TB Serial ATA Drive v/s PCIe- Flash Storage versus and desired RAM to configure.

Memory (8 or 16 GB) and storage are independent. One does not depend on the other.

The memory can't be upgraded later since it soldered to the logic board.

I would go for the 16 GB if you can afford it.

You did not identify how yo will use the mac so maybe 8 GB is sufficient.

Illaass is correct memory and storage are two different things. However there is an area where they overlap which is virtual memory.

Virtual memory is where software is temporarily swapped out to the hard disk when there is not enough RAM memory available. If you have less RAM available then you are more likely to be using virtual memory. If the hard disk is a traditional spinning hard disk (not SSD) then it is much slower and this slows down this process of swapping contents from RAM to virtual memory. El Capitan likes to use as much memory as possible so it is more likely to cause the use of virtual memory swapping. Therefore if you can only have limited RAM e.g. 8GB you can compensate for this by having faster hard disk storage.

Obviously the ideal is to both have lots of RAM and very fast storage but you may only be able to afford one or the other. Again as Illaass mentioned you cannot change the amount of RAM in a Mac mini once you have bought it but it is in theory possible to change the storage in it both by later adding a PCIe SSD and swapping it for a bigger one - or the same for the SATA storage.

You will have to decide whether you can afford to get both 16GB RAM + a PCIe SSD or whether you can only afford one of these options.