I disagree with your conclusion
I don’t see either of those symbols in the KiCad libraries, so I’m going to assume you made your own symbols or used a generic symbol - correct me if not.
Both BJTs and FETs are available (in the real world) in all combinations of lead ordering - BCE, ECB, CEB, GDS, DGS, SDG, etc. Some are more common than others, but it depends on the specific part you’re talking about.
Therefore if you want a generic TO-126 footprint that will work for any TO-126 transistor, you choose the standard pad numbering of left-to-right, 1-2-3, like it is in the KiCad library (this also matches industry standards, where they exist). This does not represent a specific transistor, it represents all transistors in a TO-126 package. Then you make/choose a symbol that has the right pin/pad numbers mapped to the base, collector, emitter, gate, drain, source pin as appropriate.
Let’s compare two TO-126 BJT symbols in the Transistor_BJT KiCad library: MJE13003 and 2SB631.
The MJE13003 KiCad symbol has the base on pin 1, the collector on pin 2, and the emitter on pin 3. Combined with our knowledge that the footprint has pads numbered 1-3 going from left to right, this matches the datasheet’s pinout for this part:
The 2SB631 symbol has the emitter on pin 1, the collector on pin 2, and the base on pin 3. This again matches the datasheet pinout:
So these two examples, at least, will map correctly to the board. It’s always possible that there is a mistake in the library, but that would be a pretty serious issue (and should be reported to the library team to be fixed).
If you’re using a transistor that isn’t in the libraries, you can either make your own new symbol, taking care to get the pin numbering right, or use one of the generic transistor symbols in the Device library: for example, Q_NPN_EBC is an NPN with emitter pin 1, base pin 2, collector pin 3.
For the KSA1381 you’re using, you said you had a schematic symbol with base on pin 1, emitter on pin 2, and collector on pin 3. But the datasheet I found for this part says it has the emitter on pin 1, the collector on pin 2, and the base on pin 3. So I think that’s your problem.