We used tools from JTAG Technology to program a flash connected to a uP in production.
It work ok.
We added the flash write signal to the jtag connector to speed up the programming. We added also termination on the data out signal and a small RC-filter on the clock signal.
The only drawback was the price
The card and the basic software were something like $2-3000.
Then if you wanted flash programming it was a additional $1-2000 and for the configuration tool of the boundary scan loop $3-4000.
As an alternative it was possible to buy the configuration from the reseller, which we did.