Can you elaborate on the ambiguity problem of Base58? I always thought that base58 was designed with this in mind as it does not include visually ambiguous letters such as "0", "O", "I", "l", etc..
That is true, but if somebody unfamiliar with the encoding writes down the characters or communicates them over the phone they have consider the case for every letter. That is a poor user experience.
None of the two examples you showed would apply to the proposed non-numeric base 46, since 0 and 1 would not be allowed.
Although it is true the potential risk may be higher, it is easy to find counterexamples where this potential risk does not matter. The 26 capital letters are easy to distinguish and allow you to use a base-26 system, while a base-2 system where the only two elements are 1 and l (or 0 and O) would be more difficult to use, for example.
