you take rest of "racial budget point" that are not used in biological traits and put them into "custom" choice.
I.E. why should jungle elves of Chult that are fighters have mandatory heavy armor proficiency, or even medium?
did they even want to use that? in that environment? maybe proficiency+expertise in Survival would be better than medium+heavy armor proficiency?
then you take background budget, class proficiency budget and what is left from racial budget into one step and get your starting proficiencies.
I pretty much agree with being able to customize the Level 1 Class features. Especially the proficiencies and training.
A less intimidating way to think about it is simply to allow "swaps". This way, the Class is what it is, and players dont need to reinvent the wheel, but swaps are possible for character concepts that require them, whether because of cultural background or individual circumstance.
You mention Chult elven Fighters are unlikely to train in Heavy Armor or even Medium. Similarly, High elven Fighters are likely to acquire a cantrip or a slot 1 per day rather than Heavy Armor. Medium Armor made out of the mithril metal and therefore Light, or Heavy made out of it and therefore Medium − would be traditional among wealthy courtiers. But most High culture Elves would rely on the
Mage Armor spell or variants of it.
Not every culture uses leather armor, and sometimes a shield for a Rogue makes more sense.
Designwise, the Level 1 of a class is very front loaded. Where each level is normally worth about a Level 4 Feat. Except Level 1 of a class is made out of a design space of two or three such Feats. Thus Level 1 includes a Level 0 of the class before gaining the Level 1. The content from this Class Level 0 represents the formative personal interest or talent, or novice introductory training, and includes features like Skill and Toolset Proficiency and Armor Training. It can be, a character that was originally training to be a Wizard but then switched to Fighter, or viceversa.
Especially for the Fighters who are "on track" to become Eldritch Knights at level 3 should already have some magical and spellcasting training at level 1. This magical training can easily be a Fighting Style option, but it might also make sense to swap out the Heavy Armor Training for two cantrips or slot 1 (typically
Mage Armor) and slot 2 per Long Rest.
Again, the simplest way to approach this is level of customization is to allow a feature swap where appropriate. It is one of the situations where for the player "you and your DM agree".
Sometimes I really wish they combine racial, background and 1st level class proficiencies(skills, tools, armor, weapons, cantrips, saves) into one pool and one and only step for character creation before "real" class features.
If D&D was more like Mutants and Masterminds, this probably would be an issue. The latter RPG requires you to buy everything from a single pool of power points (ability scores, attack bonus, defense bonus, saves bonuses, skills, feats and powers).
Yeah, I think of this as the "superhero game": pick ones powers then come up with an "origin story" for them. The origin can be because of anything: species, background, or class.
have racial traits be only non-changeable biological traits that cannot be shuffled around:
movement speed, type(swim, fly, burrow, teleport)
darkvision
Perception proficiency and/or expertise
bonus HPs
various resistances/immunities
natural weapons/armor/breathweapons/poisons
telepathy
All of these traits might be shuffled around. It depends on the specific species concept.
When a Human exhibits telepathy because of psionic, the psionic is Innate, but might express itself during adulthood, and many Humans dont exhibit the psionic trait. Meanwhile a character can acquire psionic traits because of exposure to some powerful mental influence, including from the Astral Plane. Note, the Psi Warrior presents psionic as innate but dormant, and requiring one to figure it out. Since any species is potentially psionic, it implies the soul itself (ones consciousness), which all Humanoids exhibit, is the source of the psionic power.
Darkvision can be conferred by magical ritual. Class can alter modes of movement, Perception is learned. Hit points are learned, via class experience and Constitution improvement, including the intangible aspects of hit points, etcetera. All of these traits are shufflable.
When it comes to creating a species, it strictly depends on the specific concept. There is no list of traits that every species must subscribe to.
