"Well, this was in a way my question the physical clock rate still affects shaping as a whole."
Yes and no. On a serial interface, the clock rate effects the bit transmission rate, i.e. actual bandwidth. The Ethernet "equivalent" would be 10 vs. 100 vs. 1,000 Mbps vs. etc. We don't refer to either as "shaping".
"Shaping" is when we try to emulate a lower/slower transmission media, by using a medium less often then we physically can.
Of course you've read about the usual software shaping, but on least the older 3750 platforms, it could shape its four egress queues (and?/)or "shape" it's port. The latter's description:
Bandwidth Limit Configuration:
In order to limit maximum output on a port, configure the srr-queue bandwidth limit interface configuration command. If you configure this command to 80 percent, the port is idle 20 percent of the time. The line rate drops to 80 percent of the connected speed. These values are not exact because the hardware adjusts the line rate in increments of six. This command is not available on a 10-Gigabit Ethernet interface.
srr-queue bandwidth limit weight1
where weight1 is the percentage of the port speed to which the port should be limited. The range is 10 to 90.
Notice, in the above, port is being idled for some percentage of time, actual transmission rate not being changed.
"Cisco platforms, if there's away to tune shaping by modifying the underlying mechanics of the clock rate instead of just telling the interface "transmit at line rate for x seconds and then be silent for tc-x seconds." where tc=bc/CIR"
I.e. for the 3750, above, clock rate not being changed, but yes, transmit for some time and hold for some time, although we don't configure Tc, Bc, CiR.