This ties in a little bit of canon, a little bit of stuff @mccoymostly mentioned in an answer to an Anon ask earlier, and a little bit of what’s bouncing around in Jules’ head right now.
Bones is an impeccable diagnostician. He’s an amazing clinician. He notices things. His observational skills parallel - sometimes even surpass - his technological acumen.
He’s got the newest, state-of-the-art equipment at his fingertips so that when shit hits the fan, he’s ready and able to treat every patient as minimally invasively as possible, and in order to achieve the best possible outcome for them.
He’s also old-fashioned.
Maybe it’s because he trusts his own hands more than the machines, or maybe it’s because he knows a little bit of touch goes a long way in reassuring his patients, but when time is not an issue, I feel like he falls back on a good, old fashioned physical exam. Where Starfleet hasn’t mandated how things must be done or using what instruments or methods, he takes the liberty of using his best judgment to assess and treat his patients. Where an old fashioned method would not extend convalescence any more than a modern method, he would favor that.