Encoding is basically a block of data (a sequence of zeros and ones) is represented as a sequence of electrical voltage changes (a block of symbols).
GT/s does stand for Giga Transfers per second. Here, the transfers are referring to number of symbols transferred per second, and not actual usable data bits per second.
We say GT/s instead of Gbps, because the actual usable bits/sec is determined by the encoding scheme used.
PCIe 1.0 and 2.0 encoded 8 data bits in 10 symbols (NRZ electrical signals). That's 20% overhead.
PCIe 3.0 to 5.0 encoded 128 bits of data in 130 symbols. That's a much lower overhead of 1.54%.
PCIe 6.0 (& yet to be standardized PCIe 7.0) use PAM4 for signaling and doesn't required any encoding on top –hence it is written as 1b/1b. (btw, in PAM4, each symbol is 2 bits).
You can see similar NRZ signaling with encoding in SATA, Ethernet, Fiber Channel etc. Btw, PAM4 with NRZ is used as well!
Coming to latency, latency is the time it takes for a single bit of usable data to transfer from A to B. Many factors affect this latency. Signaling medium's speed of transmission (a fraction of speed of light), signaling medium's length, signaling frequency (Mhz, Ghz etc of voltage switching), encoding scheme (encoding overhead, clock recovery or its failure and hence retransmissions, error detection/correction quality or its failure and hence retransmissions) - each of these things affect the latency of usable data.
GT/s = Signal Frequency x Bits per cycle.
Remember, PAM4 encoding in PCIe6.0 has 2 bits per cycle (2 bits per symbol).