You can't only talk about the diaphragms with microphones you also have to include the preamplification and circuitry but that's a very technical discussion compared to what I think you're asking...
Mixing and producing records is about storing all the sounds and timbres that you can create in your brain and using the best combination of these for the task at hand, and let's be clear, the term "transparent" sound is a broad term often used by companies to describe all sorts of things... just ask yourself, the flatter the curve is more "transparent" (less coloring) right? I've listened to microphones with the "flat" curves and I didn't find anything "transparent" about them, most of the time you are trying to hear what you see on the brochure, but that's not the case. Our job is to use our tools to describe the sound being recorded in the best way possible (according to our taste..). Also printing a "transparent" sound doesn't necessarily mean that it's going to be a good source to work with later in the DAW... flatter? maybe, but what can you do with a sound that is dead after pulling a -2db with an equalizer?...
Moreover, the point at which you make the decision also matters a lot. There are people making records at the time of recording and print the mix at 80% only to make minor adjustments after the print. Choosing a colorful microphone (to sort of speak the same language) is a decision that brings certain qualities into the mix. So picking a pre-amp and a microphone from your drawer is like inserting X Y Z plugins in a chain. When you start mixing you are not sure about your decisions and that's why you have to experiment, a lot, build your palette, after all, there's no such thing as a better mix, only a mix that's most flattering to the material.
Since you mention it, Digital vs Analog is a very broad topic but you are somewhat correct to think that the answer lies there, and to be clear I'm not talking about how things sound in the analog vs digital domain.
One thing most people overlook in that discussion is the workflow, which has a major impact on the result. Choosing to work in a domain with limitations and finite resources is a whole different world than working in a digital environment with virtual stuff... but no one can actually say that people working in the digital domain are unable to produce amazing results, different, but still amazing... So again, develop your style, find how you like to work, see how the engineers you like work (e.g. S.Albini would do a lot of work before printing..)
In the mixing world, we cheat, create, destroy and do all kinds of stuff all the time. It's a conversation with yourself, your aesthetics, your approach, and your overall producing style. Don't be afraid to "cheat", if you spend some time and read what was happening in the studios all these years your jaw will drop. The digital domain might never reach that level of ingenuity in terms of hosting extreme production styles...(but that's a personal opinion).
Overall I think you either lack the trust in your decisions or you're trying to find a faster/better workflow? Either way, I hope this helps :)