I'm not absolutely sure you can just stay on the train with that second ticket: it hasn't been punched (electronically or mechanically) and doesn't have the red security-check stamp. Maybe you can, but I'd check carefully before trying it.

I suppose the argument is that you pay a bit of a premium for the through-train service.

Note that the MTR does this elsewhere. Heading to Luohu, it's cheaper if you exit at Sheung Shui and then re-enter. A few HK$ saved usually, but a big saving if you're 65+.