- "In African linguistics v is commonly used as the symbol for the voiced fricative while β is used for the labial approximant."
- "So I don't use v to transcribe Proto-Berber β, because it would suggest that it is the fricative counterpart to *b."
To the first argument, I suggest that basing an orthography on the phonetic level is inevitably cumbersome because it's then prone to constant revision as new discoveries about underlying phonetics come into view. A more stable and sensible orthography is based on the higher phonemic level instead, which focuses less on exact articulation of each sound in its context but instead displays for us *distinct* sounds of the language. For example, in English, the phoneme /p/ is pronounced differently in "spun" than it is in "pat". The /p/ in the former example is completely without a puff of breath (ie. [p] in IPA symbols) since it follows /s/ while in latter example, /p/ is indeed pronounced with a puff of breath by default (ie. [pʰ]). However on the higher phonemic level, we represent in both examples the single phoneme /p/ to eliminate extra irrelevancies that are ungermane to the focus at hand. It'd be likewise unnecessary to write out every word of a proto-language like Berber with only phonetic symbols rather than phonemic ones unless the topic was specifically about the exact articulation of each sound.
It's also a fact that there are exceedingly few if any languages that contain two distinct phonemes /β/ (bilabial fricative, pronounced by blowing through near-closed lips) and /v/ (labiodental fricative, pronounced with the lower lip touching one's upper teeth). It's pointless to obsess on minutia about the exact articulation of the sound if it can be reasonably ascertained that the sound was v-like. It then suffices to take advantage of an available letter from the Roman alphabet, *v, to aid readability both by specialists and by people in general. Things should be written with clarity for both specialists *and* the general public when possible lest it encourage ivory tower attitudes, the scourge of current academia.
To the second argument, tradition indeed is a seductress but it must be rejected when it no longer clarifies but obfuscates. Sometimes tradition is misguided. Sometimes tradition is outdated. Sometimes tradition is just plain wrong. In this case, I feel that this tradition is wrong precisely because of the first argument, that orthographies should reflect the phonemic level not the phonetic and that by ignoring this rule, one has unnecessarily obfuscated rather than clarified.
Possible solutions
After reading Phoenix's explanation with deep interest, I pondered on how the system might be revised to be clearer and to follow a more consistent methodology in its design. By following the principle of phonemics over phonetics, and by reserving diacritics and special symbols for the rarer sounds of a language marked by special articulatory features, we can arrive at a more balanced and clearer phonology.
Breaking with empty Berberist traditions, emphatic sounds may be marked by the underdot, as in Proto-Semitic studies. Again, we all may quibble about the exact pronunciation of *γ (or *q) but a revised symbol *ġ has the definite advantage of visibly showing a shared feature of "emphatic" with the other emphatics which would likewise be indicated more consistently with the dot: *ḍ, *ḍḍ (former *ṭṭ), *ġġ (former *qq), *ẓ and *ẓẓ. The missing emphatic counterpart of *b, represented in this new system as **ḅ, is now impossible to confuse with non-emphatic *v which lacks the underdot. We may finally eliminate unnecessary IPA symbols and replace them with more generally readable symbols from the standard Roman alphabet that we already use while simultaneously making explicit any shared features that the different sounds may have in the language, such as "emphaticness".
And finally, through this revised system, specialists may continue to debate on the exact articulation of *ġ and such, but it won't affect the symbol shared among the specialist community until the phoneme's emphatic nature or its existence is disproven.
UPDATE
(1 hour later) Upon further thought (my mind never stops!!), enforcing a surface representation with unvoiced letters might be even more kosher and, again, this would be even more in line with what's done in Proto-Semitic linguistics. So alternatively, we could use the following symbols to clean things up: *ṭ (= *ḍ), *ṭṭ, *ḳ (= *γ), *ḳḳ (= *qq), *ṣ (= *ẓ) and *ṣṣ (= *ẓẓ).