I've no idea, it is just the way the manufacturer decided to do it. Often the collector is bonded to the center wire so the other two connections, which are layered above it in the silicon, can leave with one bond wire on each side. If the base was in the center and was providing mechanical support as the wire does, half the silicon would be on one side and half of the other so two dies would be needed.
I have an education - engineer for production of semiconductor devices and IC. Manufacturers to optimize the topology of the crystal to improve the performance and reduce chip area. Accordingly, when installed crystal in a standard case, of the crystal it is convenient to connect the pins in a particular order. Over time, the standards developed pinout for interchangeability of parts in the diagrams . But to come to a common standard is impossible because of the large difference in topology of some crystals . Therefore, there are exceptions.
In googled met the information that 2SC535 has an analog NTE107. Do NTE107 pinout is the same.
I use transistor tester for questions like this. Low cost model with 16x2 display. Very useful device! It can measure transistors (bipolar, mosfet), diodes, RLC-meter. On russian radio forums I seen circuit and new firmwares for microcontroller of this device.