We know that engineers aren't really going through and figuring out how to make it so the Avatar's medium lasers aren't hardwired in, but to say "yeah, you can swap those out for extra heat sinks now" feels cheap. I had always figured that things that were hardwired in were that way for a reason.
I've vague recollection those are because the targeting system had issues. Perhaps the computer had limits how many pod-weapons it could handle?
No doubt solvable problem, but at the time the Kuritans probably didn't have time to spend on fixing relatively small issue (two medium lasers are never a bad thing), and later on it would require modifying production lines and/or existing 'Mechs, plus it would be to solve a problem that isn't really even a problem.
In-universe, most fixed components are probably either for role reasons (the Mist Lynx is intended to be a recon-capable design regardless of its config), or because there's some engineering issue that is best solved by leaving equipment fixed (for example, suppose there's no space for a weapon pod where the Adder's flamer is, but gyro is already calibrated for 16 tons, so they have half a ton over... and non-podded flamer can be worked into the design.)
EDIT Just to be clear, i'm talking about physical, real space, not the abstracted record sheet slots. Assume the 'Mech's mostly designed already and there's no way it can modified to include one more pod at this stage. After all, a podded weapon is self-contained with overall shape being something akin to a box, whereas a fixed weapon might be weirdly shaped and be fitted into places where a pod cannot be (like under the cockpit/"nose" in the Adder).
In real life: "Don't think about it too closely", and "game mechanical necessity, otherwise you erase the difference between standards and Omnis".
Personally i like fixed equipment in Omnis, it can inform the intended role or serve as a backup weapon that allows me to focus on designing config around primary purpose. Plus it gives character, otherwise Omnis tend to be pretty... well, boring, since they're rather similar to each other when empty. Obviously fixed equipment goes against the concept in a way... but they do occasionally give a reason for another, different, later OmniMech.
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Now, on the actual topic, pretty sure somewhere it was stated that (Inner Sphere or Clans, can't recall) usually the unit commander decides what pilots under them will be using. Depending on the conflict/trial scale, a Star Commander might designate configurations for warriors under their command, or perhaps a the commander of a Binary or Trinary or Cluster would order certain Stars for certain roles (eg "Alpha Star will be equipped for long-range missile support, specifics to follow").
I'd assume that actual individual configuration is a rank privilege in combat operations, or a granted privilege ("Warrior ABC has potential to be a ristar, they can pick what they want"). Trials are naturally an exception, depending on the clan, even cadets might be able to pick their own configs for training scenarios or their Trial of Position.
Of course, the Clans being what they are, it is plausible a Warrior could demand a Trial of Refusal over being ordered to use a specific configuration, though this would be bad form during actual combat (but before a routine patrol or some such, why not).
Probably the same within the Inner Sphere, but no option to disputing ordered configuration. Privately owned OmniMechs with privately owned podded-weapon collection might be an exception, though insisting on using direct fire weapons for a missile support mission probably isn't too smart.