I travelled on the 1609 from Axminster to Castle Cary yesterday (it was quicker to go that way to Bristol than my normal route via Exeter). For some reason there seemed to be a built in stop at Chard Junction even though we didn't pass anything and used the fast 'up' line (as far as I know Chard Jc has bidirectional lines, with the down line being used for the first train in either direction so the second train may not have to stop). As the train was scheduled to take 27 minutes to Yeovil from Axminster, this seems to have been built in.
I think Yeovil Junc - Pen Mill is token worked as is Pen Mill-Castle Cary, as the train had a few minutes wait at Junction before a scheduled stop at Pen Mill to collect tokens. It had a pretty meandering 64 minutes scheduled from Axminster to Castle Cary for what's a journey of about 37-ish miles. But that's engineering works and single line working for you.
The reason for the stop at Chard was to allow the Waterloo train ahead to clear the section between Chard and Yeovil.
Also the reason for the huge amount of time between Yeovil and Castle Cary is because the
HSTs▸ are limited to 40mph compared to a
DMUs▸ 75mph on the section between Pen Mill and Castle Cary.
Hope that clears everything up for you.