A single current generation Thunderbolt port runs two separate 10Gbit channels. Each channel is a mux of PCI-E data and a DisplayPort 1.1a stream. Two displays (each up to DisplayPort 1.1a's 8.64Gb maximum bandwidth) can be driven on one chain, one off of each channel. This can either be two Thunderbolt displays or one Thunderbolt display and one pass through raw DisplayPort display at the end.
Some restrictions apply due to the need for one Thunderbolt controller chip per display to do the DisplayPort demuxing. A Thunderbolt monitor will typically have one Thunderbolt chip and will use its DisplayPort output itself. A DisplayPort display can't be daisy chained directly after a Thunderbolt display (but can after a non-display Thunderbolt peripheral) for this reason.
It sounds like (according to the OP article) that the 2013 Thunderbolt chips (Redwood Ridge) will allow DisplayPort 1.2 pass through only. In this configuration the port could either be run as a Thunderbolt chain (with the above limitations to 2xDP 1.1) or as a DisplayPort 1.2 port. In 1.2 mode Thunderbolt peripherals couldn't be used, but DisplayPort 1.2 features (in particular 4k support and MST) could be used. Presumably the 2014 20Gbit channel Thunderbolt could allow 2xDP 1.2 as that tops out at 17.28Gbit.
Edit: yes, this means that devices sharing the chain with two Thunderbolt displays will have constrained incoming bandwidth. Probably even more so as the only Thunderbolt displays in existence also sport USB, speakers, a webcam, FW800, and Gigabit Ethernet, which together could easily eat up the remaining bandwidth on the TB channel. This may also be part of the reason why Apple hasn't released an updated Thunderbolt display with USB3, 2x10Gbit doesn't go very far with a pair of 27 inch displays hogging most of it.