Does a Ranger's Companion get proficiency bonuses twice on its skills?

Question

A Ranger's Companion (PH p.93) enjoys the following bonuses relative to a typical member of its species:

Add your proficiency bonus to the beast's AC, attack rolls, and damage rolls, as well as to any saving throws and skills it is proficient in.

1. In the case of skills and saves, does the Ranger's proficiency bonus replace the normal +2 proficiency bonus a CR ¼ beast is entitled to (MM p.8)? Or do the two proficiency bonuses stack instead?

2. Does the Ranger have to be present to grant these bonuses?

Answer 1

The answer to your first question is that you're...kinda overthinking it. Every animal the Ranger can have as an animal companion has a statblock with numbers calculated for you. The proficiency bonus is added to those numbers. You don't actually need to know or care about the proficiency bonus of the animal, because it's not something players are assumed to know about.

The ability doesn't say anything about the Ranger needing to be present, so they don't need to be. The bonuses are granted for being an animal companion, so the animal companion always has them.

Answer 2

PHB 173

Your proficiency bonus can’t be added to a single die roll or other number more than once. For example, if two different rules say you can add your proficiency bonus to a Wisdom saving throw, you nevertheless add the bonus only once when you make the save.

So your proficiency bonus replaces the creature's.