This seems to be a 5v SD card holder but the Electron runs on 3.3V (as do SD cards natively)
For native 3.3V devices you don’t need or want a card holder with level shifting.
But with this board you need a supply voltage of 4.5~5.5V which the LiPo won’t deliver.
A3~A5 is SPI not SPI1.
SPI1 maps to these pins
SS => D5 (default)
SCK => D4
MISO => D3
MOSI => D2
I am kicking myself right now very hard after wasting months on this problem.
I am sure my reader was advertised as both 3V and 5V and I am fairly sure when tested with Arduino I tried it on 3.3V knowing the electron was 3.3V
Anyway just though ok lets try it on 5V and it now works.
Feeling rather stupid, voltage requirements is basic stuff.
Thanks ScruffR for you very fast and accurate reply