Yes.
Proficiency isn't tied to anything except your character level (i.e if you multiclass for example Rogue 3 / Cleric 2, your character level is 5, which means your proficiency bonus is +3).
Your proficiency bonus increases everything you're proficient in, full stop. This applies to attacks with weapons you're proficient with, saving throws you're proficient in, skills you're proficient in, etc.
From the Basic Rules, p. 7:
Proficiency Bonus
The table that appears in your class description shows your proficiency bonus, which is +2 for a 1st-level character. Your proficiency bonus applies to many of the numbers you’ll be recording on your character sheet:
- Attack rolls using weapons you’re proficient with
- Attack rolls with spells you cast
- Ability checks using skills you’re proficient in
- Ability checks using tools you’re proficient with
- Saving throws you’re proficient in
- Saving throw DCs for spells you cast (explained in each spellcasting class)
Yes
Your companion uses your proficiency bonus rather than its own.
It is important to note that it says, without condition, that the companion uses the Ranger's proficiency bonus. This means that, from this point on, it's proficiency bonus is the Ranger's proficiency bonus. Think of it as erasing the value on the creature sheet, replacing it with the Ranger's value, and then recalculating everything from there.
Upon looking at the UA document again, this is further supported as such:
Keeping Track of Proficiency
When you gain your animal companion at 3rd level, its proficiency bonus matches yours at +2. As you gain levels and increase your proficiency bonus, remember that your companion’s proficiency bonus improves as well, and is applied to the following areas: Armor Class, skills, saving throws, attack bonus, and damage rolls.
While the wolf has a listed proficiency bonus of +2, nowhere is it stated that this bonus is already included in the damage of the wolf's attack. We may infer that this damage is from the wolf's DEX mod, as is supported by the fact that the base to hit is +4, which would be +2 from proficiency and +2 from DEX, matching expectations for standard application of proficiency bonuses. The wolf's damage should be increased by a flat 3 points, making the roll 2d4+5, the same as you have stated. Furthermore, applying +3 to the base 13 also matches your stated 16 AC, and replacing the +2 with proficiency with +3 also results in a +5 to hit when added to the DEX mod. It is not explicitly stated that the bite is a DEX-based attack, but this is the only value that makes sense from the creature stats. Your math looks right.
Bonus Answer: No, the damage dice of the wolf's bite attack do not scale. It is important to consider that the wolf companion is not intended to be as powerful as an extra PC, but is instead part of the power of the Ranger to whom it belongs. Applying proficiency bonus to a damage source is a benefit other classes do not have, and this comes from an attack that does not require the use of any of the Ranger's actions. Also, consider that this attack has the potential to knock a target prone, leaving it more vulnerable to melee attacks until it has the opportunity to stand. Such a tactical advantage is certainly not weak.
Best Answer
Option 1, increase the bonus anytime you increase your proficiency, even if you do not have access to the infusion (so +1 at level 5, +2 at 9, etc)
The Battle Smith's Steel Defender also has the Might of the Master feature, is obtained at level 3, and is fairly similar to the Homunculus Servant. This answer is mostly based on logic, as the wording is ambiguous (as you have noticed).
First of all, consider that the text below makes no mention of you having to have learned the Infusion previously. At level 3, even if you haven't learned the Infusion, the Servant's stats increase. They also increase even if you do not have it summoned when you level up.
Secondly, consider that, if stats only increased after you learned the infusion, it would cause two seemingly bad effects: a PC would be forced to take this infusion at level 6 if the PC indeed wanted it; and a multi-classed PC would also be forced to take 6 levels of Artificer to learn this before accumulating other levels.
Thirdly, DnD 5e focuses a lot on simplicity. Option 2 would make you have to register when you had learned the infusion, to count proficiency bonuses from there. It's much simpler to just assume the proficiency of the Servant is the same as yours, period.
That being said, many features in the class are poorly worded. I expect Sage Advice to make an Artificer specific compendium soon.