The master-slave arrangement doesn't strictly solve the metastability issue, AFAICT. It is commonly used to cross over between different clock domains of synchronous logic, but I don't quite see what improvement it does on purely asynchronous input (the slave gets a clear state, but it may be derived of a metastable transition anyway). It could simply be an incomplete description, as you could add a hysteresis function by combining the outputs of the two registers.
As for the differences between SR, JK, D or even T flip-flops, it tends to boil down to which inputs are asynchronous. The simplest SR latches do not toggle with S=R=1, but simply keep whichever state was kept last (or in the worst case, oscillate with a gate delay), that's the race. The JK, on the other hand, will transition on the clock edge - synchronous behaviour. It is thus their nature that a T register can only be synchronous, and an asynchronous D latch is transparent while latching. The SR register you describe doesn't have the T function, which can be useful depending on the function. For instance, a ripple counter can be described purely with T registers. Simply put, the JK gives you a complete set of operations (set, clear, toggle, and no-op) without costing an extra control line.
In synchronous logic, we frequently use wide sets of registers to implement a larger function. It doesn't strictly matter there if we use D, T, JK or whatever registers, as we can just redesign the logic function that drives them to include feedback (unless we need to build that logic - i.e. in 74 family logic). That's why FPGAs and such tend to have only D registers in their schematic representations. What does matter is that the register itself introduces the synchronous operation - steady state until the next clock. This allows combining plenty of side-by-side registers or ones with feedback functions.
As for the choice between delayed-pulse and clock-synchronous logic, it's not an automatic one. Some early computers (f.e. PDP-1) and even some highly energy efficient ones (f.e. GreenArrays) use the delayed-pulse design, and it is in fact comparable to a pipelined design in synchronous logic. The Carry-Save adder demonstrates the crucial difference - it's a pipelined design where you actually don't have a known value, not even intermediate, until the pulse from the last new value to enter has come out the other end. If you know at the logic design stage repeated accumulation but only the final sum is used, it may be the best choice. Meanwhile, FPGAs are typically designed with only a few clock nets and therefore do not adapt well to delayed-pulse logic (though it can be approximated with clock gating).
I hope this is more helpful than further confusing... interesting questions!
Define divide by 1 clocks on the and_* nets and declare them to be physically exclusive. Cadence RTL compiler handles the situation correctly by generating 3 timing paths for registers clocked by cpu_clk (one path each for one clock). Registers directly driven by clk0, clk4 and clk_ext have their own timing arcs.
create_generated_clock -source [get_ports clk0] \
-divide_by 1 -name and_clk0 [get_pins and_cpu_1/Y]
create_generated_clock -source [get_ports clk4] \
-divide_by 1 -name and_clk4 [get_pins and_cpu_2/Y]
create_generated_clock -source [get_ports clk_ext] \
-divide_by 1 -name and_clk_ext [get_pins and_cpu_ext1/Y]
set_clock_groups \
-physically_exclusive \
-group [get_clocks and_clk0] \
-group [get_clocks and_clk4] \
-group [get_clocks and_clk_ext]
Best Answer
Clocks are used in computers for the simple reason that most if not all of the circuity is synchronous sequential logic.
Now, that may not seem satisfying and granted, you would reasonably ask "why are synchronous circuits used in computers?" but that's an easy question to answer too:
An active area of research is asynchronous computing where most if not all of the circuitry is asynchronous sequential logic.