Can better parts.....

They can most certainly in the hands of a skilled craftsman that understands the overall design case by case, but no guarantee in general. The devil is all in the details.

I would expect a difference in sound with the specific combo the OP relates, most likely for the better, but only if done well by someone who really knows what they are doing.

Parts are just parts. Its what is done with them that always matters.

I would recommend that for whatever cost might be involved for any particular custom mod, especially pricey ones, options to replace or upgrade to different well received high value gear be considered as well. Sometimes better results can be achieved more easily replacing rather than tweaking. All surgeries usually come with some amount of risk.

If you know what you are doing, and correctly replace specific parts with other "Higher quality" equivalent parts electronically (like a capacitor of equivalent specification), I would expect only positive results. That's always how good things might become even better.

The question will always be how much and is the investment a good one.

That's not always a question that is easily answered, but if one can answer it with confidence, and not put things at risk otherwise, for example by voiding a manufacturer's warranty in the process, have at it.

When one party modifies another's device, that always leads to questions regarding whose problem it is if something goes wrong. ie who ends up paying to get things fixed.

Then there is always the resale value aspect of things as mentioned. Modified devices can be hard to categorize and resale value can be nebulous and even negatively affected accordingly compared to more "known quantity" type items.

Personally, I shy away from buying most anything that has been modified by a third party used, especially if pricey. I prefer to invest in more known quantities that have been positively received by many. In other words, the maker got it right for my purposes right out of the box.

I'm not saying don't do it, rather just be aware of what one might be getting into before pulling the trigger, especially with a third party mod as opposed to doing it yourself and knowing what you are doing.