Why location of CT is different for the two Circuit breakers in same substation layout?

For element protection (line, transformer etc) it doesn’t matter which side of the breaker the CTs are on.

It does matter for breaker failure protection.

EDIT: Adding explanation.

The upper figure below shows the CT and VT connections to a distance relay for typical transmission line protection. For faults on the transmission line, the relay will be presented with the same quantities whether the CT is on the bus (S) side of the breaker or the line side (lower drawing).

However, the CT location will impact breaker failure protection. There are different flavors of breaker failure but one of the most common is simple logic as shown below. So, when any line protection element in the relay (RS) tries to trip the breaker the top input to the AND gate asserts. The other input (50BF) is a simple overcurrent detector that measures current in the breaker from the CT. If both inputs are asserted for a short time delay (TD, typically 7-12 cycles) then a "breaker failure" event is declared and breaker failure action taken (usually tripping additional breakers behind this guy and possibly sending transfer trip signal to remote end).

Now, if the CTs are on the line-side of the breaker and the fault is actually inside the breaker (or a fault develops internal to the breaker after the line fault is cleared) then the current measured by 50BF will be zero (assumes remote end has properly opened for the original line fault). That is why the CTs for the line protection should be on the bus side of the breaker.

Further, any bus differential CTs (not shown here) would be located on the line-side. This way we have 2 protections overlapping at the breaker (bus differential and line protection/breaker failure).