Tom was annoyed because he didn't want to sort through 37 varieties of tomato soup. He didn't care- he just wanted food.

They are, it just takes time to update, since it gets sent over whenever the computer gets updated.That’s why Tom Paris was annoyed that the Voyager’s replicator didn’t have his preferred tomato soup ready. It was scheduled to be loaded onto the computers on Tuesday.

Patterns might be portable on storage devices, but that doesn't necessarily mean they're cross-platform, especially cross-species/technology, or maybe it would require a technical specialist to convert the pattern between systems.

I can absolutely see this being a thing in Star Trek life. You find specific versions/recipes that you like and save them to a personal data storage device, and then when you transfer to a new command you put in a request with the local IT department to have your recipes loaded into the replicator system, which takes some time because they have to review them for safety (no malicious insiders uploading weapons labeled as "grandma's chicken soup") and maybe convert the pattern to work on the local replicators. There's a support ticket queue for that, submit your files and take a number, we'll get to you when we can.

You can write the pattern yourself, but it is easy to get them wrong (Janeway managed to have it consistently produce charcoal).

Absolutely, or probably try to arrange a new meal pattern using information on previously scanned & stored items. But yeah, it would require some specific knowledge and skill to get right. In the present, you can download lots of 3D-printable objects from the Internet, or if you know how to model you can design your own - the second is a lot more complicated. Most people would probably just use existing replicator patterns.

So, I've been thinking about this and finally realized I need to RTFM:

lets say, the materials are all scanned down, and they just tile them to fill in what ever part you’re trying to fabricate. lets say they’re 1 cm3 cubes of materials. sure, the computer could tile those cubes digitally, and then cut them back into the shape you needed. But, how do you handle the gaps between the blocks? you could fill them with procedurally generated molecules/atoms, right?

So, kind of. Page 91 says "The chief limitation of all transporter-based replicators is the resolution at which the molecular matrix patterns are stored" and "extensive data compression and averaging techniques are used" which results in "single-bit inaccuracies".

I think the implication is that objects are reproduced in essentially arbitrary blobs/fields which are of uniform molecular patterns (e.g. the flesh of an apple being distinct from the skin, the stem, or the seeds) but not in blocks/voxels.

you wouldn’t need to scan materials. You can just model the atoms and procedurally generate the bonds, and then tell the replicator how to print the damn thing.

The problem is that specifying the exact molecular structure of something complex like, say, a soufflé, would be extremely difficult and time-consuming to do manually, and probably it still wouldn't taste or feel right when you ate it - imagine trying to reproduce a Monet by specifying manually in lines of code where each drop of each color of paint was placed on the canvas, without being able to see the finished product until you hit "print" - it would take you years, maybe decades to get it right. Getting the texture and flavor of a grilled chicken breast right would be insanely difficult to do by specifying each atom in the whole structure from scratch. Scanning a real one would be a much easier path to acceptable reproduction, hence: "a quantum geometry transformational matrix field is used to modify the matter stream to conform to a digitally stored molecular pattern matrix." (Treknobabble but the point being that a thing is scanned and the pattern stored digitally for later reproduction)

we know what an iron atom is and can model it.

So yes, especially for industrial applications such as your example of a uniform steel bar, but for things with complex chemistry and physical structure it's too difficult to specify from a "first-principles" perspective and get something that you actually want to eat.

Maybe a higher-grade, specialized food replicator could generate food items procedurally as you suggest, or maybe it would just have a group of stored patterns for the same item that it would randomly select from (probably easier) so that the output isn't always the same, but probably the standard Starfleet model doesn't do this as it would be more of a luxury feature.