It depends what you mean by "transparent"? because I'm having difficulty understanding the term as it can mean many things. My own interpretation is that transparent simply means high fidelity/less noise, my confusion comes from trying to relate the word to music:
transparent
• adjective 1 allowing light to pass through so that objects behind can be distinctly seen. 2 obvious or evident.
— DERIVATIVES transparently adverb.
— ORIGIN from Latin transparere ‘shine through’.
It means, or my understanding at least, is twofold:
It lets the source (guitar, duh) or any other tone shaping thing involved (amp, pedals etc) sound like they sound like without adding its own sound. This applies, to my mind, to things like modulation effects, where you want the modulation effect but may or may not want any changes to the core tone in the process. When this meaning (as I take it to be at least) is applied to amps and pedals, I laugh. Ever plugged a guitar into a totally (or near as) dry and flat input and listened through something designed to be really, genuinely (in theory) transparent, like monitors? Practically unrecognisable. Amps shape tone, a lot, all of them, even cleans.
It lets the details of your playing, nuance of pick attack, vibrato, and what have you come through. it doesnt over-manipulate the input such that those things are suppressed. I like this to be the case with all my kit and it seems to me that it applies to everything musical (gear wise)