The suggestion to look at the keyboard with xev led me to identifying the likely issue (see https://unix.stackexchange.com/questions/552680/why-does-hypertab-not-work-tested-in-ubuntu-gnome-and-xfce). In particular,
xmodmap -pm
showed that mod5 was overcrowded, where my modifications had been included with the default map (for the xkb US keyboard layout) of:
mod4 Super_L (0x25), Super_R (0x86), Super_L (0xce), Hyper_L (0xcf)
mod5 ISO_Level3_Shift (0x5c), Mode_switch (0xcb)
to give
mod4 Super_L (0x25), Super_R (0x86), Super_L (0xce), Hyper_L (0xcf)
mod5 <OTHER_KEYS, inc. Hyper_R> ISO_Level3_Shift (0x5c), Mode_switch (0xcb)
So ISO_Level3_Shift was triggered along Hyper, and thus didn't work.
However, by setting to Super, and then using different mod numbers, Hyper works as advertised. For details, see writeup here: https://github.com/bjohas/Ubuntu-keyboard-map-like-OS-X/blob/master/Hyper%20key.md