Well.........
I just tried it, and you're right! Boot from softmod, turn the Xecuter 2.6 on, and you can flash it with either Evox or FlashX. I didn't have Raincoat to hand, but there's no reason that shouldn't work either.
Hmmmmm..... scratches head..... I'm sure it didn't work last time I tried, that's one of the reasons I bought a programmer......!
Maybe it's just the other way round that doesn't work - boot from chip then flash TSOP. I'll try that when I get a spare hour to put a chip in a flashable box.
Ah - or maybe it's because my Xecuter 2.6 is in a 1.6 Xbox with no TSOP, so there's only one place to flash. I'll try it again in an Xbox with a flashable TSOP, see if I get the same results.