Scripts like prefix-free can make coding faster since you don’t have to add all those prefixes manually. Even if you are using a CSS pre-processor or using something like prefixr to add the prefixes later, prefix-free is probably still faster since there are no additional steps or extra code.
In terms of how much time it takes for the client to download your code this depends on how many prefixes are needed in your CSS. Prefix-free is 2kb, the additional code you would need for “pure CSS” might be more or less than that.
Lastly, “pure CSS” would render faster than using prefix-free, but the difference might not be noticeable.
prefix-free does have a few issues so ideally the prefixes should be in the CSS, but then again prefix-free offers a great convenience.