IMO with packraft and feet there nowhere you cant go in Scotland. Just look at a map, the lines of the lochs and string it all together.
I’ve not tried it, but my feeling is that the extra ~13kg of a bike on the boat complicates things unless you’ve designed a route specifically for a bike and are doing steady paddles with little portaging or rough, unrideable ground (eg: along lochs then picking up roads and tracks). Cross country, walking is much more versatile. I agree a packraft would be wasted on most of the Great Glen. Better to go where regular boats can’t.
You can’t go wrong with the two coast to coast routes out of Mallaig (train): up loch Morar and over to Arakaig, walk over to Loch Lochy and down that river to Ft William (1 portage). Then from FW paddle round (tidal) or follow the C2C walk route to Blackwater res, or on over to Loch Laidon, and down Rannoch and Tummel lochs on down the Tay river (various portages I believe) to Perth. I’ve done that as far as Rannoch Moor.
Or from Loch Lochy/Gairlochy, walk any way you like over to Loch Laggan and hop onto the Spey around Aviemore and down to Speymouth/North Sea. We did Spey in IKs and folders one time, but it would be great ride in a packraft too.
Both will be about 10 days, I’d guess. I’d then go up to Ullapool, get a bus up the A835 a short way and spend a few days in the Inverpolly Area. It doesn’t go anywhere but there are some great mountains all around.