According to the technical advisers to the show, by way of the TNG tech manual (non-canon),
something does go into the replicator, a sterile organic goo from a holding tank.
Which just might explain the finished product's taste.
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Key phrase: 'non-canon'.
Replicators were REPEATEDLY stated to convert Energy into Matter and there was 0 mention on-screen that they use organic mass/raw matter of any kind to make anything.
And if you bring up Ds9 and how we saw some kind of matter being splurged when they were fixing a replicator - keep in mind that those were Cardassian replicators, not Federation, and it was a malfunction - other situations in cases of malfunctions demonstrated that things appeared in systems where they didn't belong - so the Ds9 singular example of a 'leaking pipe' is 0 proof.
Also, even if raw matter WAS involved (and by on-screen evidence/statements it's NOT) nothing would affect the product's taste.
Because it would be broken down into base elements, then reconstituted into something entirely different... once you get rid of the original by breaking it down into base elements and you rearrange them to suit your needs, it no longer 'tastes', 'feels' or 'smells' like the thing it was before (because you just formed a new molecular structure).
But this process of breaking down matter into base elements and reconstituting them into new matter was done in Archers and Kirk's era before the invention of replicators, and even WE can do it.
The way energy to matter transformation probably happens is on the subatomic scale through rearrangement of particles.
The plasma that runs through the EPS grid of the ship probably contains base elements in abundance (they would likely use a form of energy which would for all intense and purposes be 'convenient), which makes it an excellent source (it's constantly generated so long as the Warp core is active and the system is supplied).
The replicator merely takes needed energy, and re-assembles those readily available base elements into matter at a command.
It stands to reason they would be energy intensive as a result (at least until Voyager got the technology in season 7 to triple their efficiency and reduce the power consumption by half - of what they were using while they were in a Void which forced the ship at the time to consume 10x more power than outside of it).
Archer's and Kirk's era way of producing foods and materials was probably done (as previously mentioned - plus it was in fact directly inferred) via heavy recycling (which would entail breaking down existing matter into base elements and then reconstituting them into something else) and selective growth of specific protein based organs (synthetic meat with all the nutrients if not even more so - there would be 0 need for slaughtering animals even before Archer's Enterprise NX-01 was launched - so I really don't get why a lot of people tout that replicators would eliminate a lot of things - they are just a step up from what was done before- and a more efficient/cleaner way of doing it).
Your argument that replicators create 'flawed' food is flawed by itself, because it's only been mentioned on FEW instances (2 or 3 at best) by selective (and again FEW) characters who stated the food 'doesn't taste right' - which can be interpreted in MANY ways... the first one that comes to mind was that it tastes different to those specific individuals, because they probably grew accustomed to food which has been PREPARED in a different way.
The replicator has a pattern for how a certain meal is done in a 'generic way' - therefore, a person would probably have to 'slave over the replicator' so to say in order to get the taste right because they would have to fiddle with the existing pattern so they can add or remove certain things to 'get the taste right'.
Kim for example replicated his mom's Apple pie, and ended up saying 'it's good, but would have tasted better in San Francisco'.
Psychological effect at work, nothing more.
Also... vegans can still exist even if no animals died to supply your meat.
How?
They could be disgusted by meat itself for one thing (as Vulcans apparently are).