It's been my observation that many of the older clip-on tuners were more prone to mark the finish on the headstock than the latest generation of tuners. Partly, this is due to the use of less finish-hostile materials on the newest tuners, like silicone pads, instead of butyl rubber ones. And partly, this is due to less pressure from the mounting clips.
As for leaving the tuner on, even during public performance, all I can say (quoting Dylan) is that "the times, they are a-changin'!" It is no longer considered a faux pas to leave your tuner on the instrument while playing or performing. The etiquette has changed. In fact, it is taken to be a sign of respect to the music, and to your audience, to keep as well-tuned as possible! This is not just true of modern folk performances: it is increasingly common to see tuners on the headstocks of classical guitars in concert, for example. I attended a performance, before the pandemic, at the Aspen Music Festival, where a classical guitarist performed with a flautist, and the guitarist had a tuner mounted to his headstock -- unapologetically. In fact, it was a popular Snark brand tuner.
There are countless examples of this now (check out YoutTube if you don't believe me). Electronic tuners are here to stay, and not in case compartments. They are getting smaller and smaller, and therefore less intrusive visually, and also less "finish-hostile," as mentioned earlier. So, it's now easier then ever to mount a tuner on an acoustic instrument during live performance. As for electric (and electrified) instruments, these have had tuners available in the electronic-effects chains for a very long time. No one, to my knowledge, has ever complained about the use of these in performances.
No two ways about it: tuners are a fixture of modern acoustic music. There is no real need to constantly mount and dismount these. I realize that some self-described "old folks" here in the Mandolin Cafe are bothered by the aesthetics of tuners clipped to headstocks. I'd urge them to try to get over it! They're not that ugly, after all, and they are incredibly useful. And in the future, ever-smaller electronic tuners may become permanently mounted to the backs of headstocks, or discreetly placed in other places -- perhaps they'll even be incorporated permanently into the next generation of tuning machines. And no one, to my knowledge, has ever complained about an instrument being too well tuned!
Meanwhile, check out this four classical guitar concert on NPR, and every single guitar has a tuner mounted:
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