I wonder if it isn't so much the transformer as much as it is the user. In my experience, the conventional bell & whistle "morse code" can be tricky to time correctly without some practice as indicated in the example manual. I can't say I have personally tried it with a CW or GW. As @Adriatic stated, the CW80 and GW180 are of similar construction & circuitry and I wouldn't expect a different result based upon the design. My Lionel Legacy PowerMasters have these codes built in and they work flawlessly, so Lionel isn't being malicious.
Here is a non-exhaustive list of the codes (the manual goes into more detail in the next few pages):
