Li Shenron
Legend
I am not sure how II also think that gaining crucial proficiencies at level 3 is too late (see scout). I really do believe that at least you need to remove the addition (if you don't already have it) which forces you to not take the thematic proficiency because it would be wasted. Interestingly dndbeyond ignores the if clause in the character builder and just allows you to chose a different proficiency as by the standard rules.
I guess chosing the sublclass at level 1 would work better for the artificer would get rid of the problem.
This.
Not only moving the subclass to level 1 would fix the delayed proficiencies oddity, but it would also push spellcasting to 2nd level, fixing the other oddity of a non-standard half-caster spell slots progression. Cantrips can still start at 1st, as they are unprecedented to half-casters. Then maybe move Infuse Item to 3rd:
1st: Magical Tinkering, Artificer Specialist*, Tool Expertise
2nd: Spellcasting
3rd: Infuse Item, Artificer Specialist feature*
*The Homunculus/Turret can stay at 3rd level