I removed the pedal fulcrum pin. It made a big difference to lining up the diaphragms. The pump works a whole lot better now, although it still leaks at the very bottom.
Thank you Jolene.
I remember a friend saying that a trick of manufacturing used to save materials is to slightly fill in moulds to reduce their volume. This may be happening here. I found that the
diaphragms are different depths of around 300 micron. Not that my calipers are high quality, but I didn't move the caliper between measurements.
The side by side photo shows the difference.
--The second backup pump.--
On the second newer backup pump I decided to repeat the process of pin removal and test it, but gave up in the end as I it is just such a fiddle to make the diaphragm line up on he pedal side. Harder than the old one was. I think something has slightly changed in the manufacturing. Also I am looking at the poor quality of spares. I am going to try the Whale Gusher foot pump soon. I'll just put up with these leaky TMC pumps for the moment as they work somewhat well enough.
We can also see that the diaphragm does not reach the plastic base when placed over the lip it's supposed to seal to.

Seal A

Seal B

Very thin at base diaphragm holding point.
Knocking out fulcrum pin.