As of 2019, the new Sage Advice Compendium clearly states that they don't interact.
These aren't allowed to work together on a single check.
Can the rogue’s Reliable Talent feature be used in conjunction with Remarkable Athlete or Jack of All Trades?
No. Each of these features has a precondition for its use; Reliable Talent activates when you make an ability check that uses your proficiency bonus, whereas the other two features activate when you make an ability check that doesn’t use your proficiency bonus. In other words, a check that qualifies for Reliable Talent doesn’t qualify for Remarkable Athlete or Jack of All Trades. And Remarkable Athlete and Jack of All Trades don’t work with each other, since you can add your proficiency bonus, or any portion thereof, only once to a roll.
An earlier Jeremy Crawford tweet restates this:
Making sure this is clear: these features work together on a character. They don't work together on the same ability check.
This is definitive, and contradicts earlier apparent rulings, i.e. from the 2017 SA compendium.
I can't see this imbalancing your game, but be cautious of favoritism/unfairness and stepping on the toes of Bard/Rogue
There are a great many features that grant proficiencies with no exceptions made for people who are already proficient in those things; as such, I would be cautious of making a change to this one Warlock feature and not the various other features as well.
Something else to keep in mind is that Expertise is mostly unique to Rogues and Bards so giving it to other classes might be stepping on their toes even more.
Also note that the Unearthed Arcana version of the Squat Nimbleness feat granted doubled proficiency if you were already proficient, but in its final release in Xanathar's Guide to Everything this was removed and replaced with advantage on checks to escape grapples. That doesn't necessarily mean the doubled proficiency was bad but for some reason they did remove it.
Proficiency-granting features do a lot of different things
This is more just on overview of the various options available and their rarities.
Most features just grant proficiencies with no exceptions
I went through a list and the majority of proficiency-granting features do not have exceptions for those already proficient. This includes most of the feats that grant any sort of proficiency as well. Below are the few exceptions I was able to find:
A few features besides Expertise double your proficiency bonus:
The Scout Rogue's Survivalist feature grants them two skills proficiencies and a doubled proficiency bonus with those skills.
The Knowledge Cleric's Blessings of Knowledge feature grants them two skill proficiencies and a doubled proficiency bonus with those skills.
The Purple Dragon Knight Fighter's Royal Envoy feature grants them proficiency in Persuasion. If they are already proficient in Persuasion they can pick a different skill. Regardless, they get a doubled proficiency bonus with Persuasion.
The Prodigy feat is the only feat that lets you get doubled proficiency bonus on a skill.
A few features actually grant different proficiencies if you already proficient
The Artificer subclasses grant a tool proficiency, but if are already proficient in that tool you can pick a different one.
The Samurai Fighter's Elegant Courtier feature grants proficiency in Wisdom saving throws, but you can pick a different one if you already have that.
The Gloom Stalker Ranger's Iron Mind feature grants them proficiency in Wisdom saving throws, but you can pick a different one if you already have that.
Somewhat related, a few features that grant darkvision extend your darkvision if you already have it. Most features that grant darkvision do no such thing.
Similarly, a select few features that grant spells give you different ones if you already know them. Most features that grant spells do no such thing.
What I do at my own tables
When people end up acquiring a feature that grants them a proficiency they already have, I allow them to pick a different but thematically similar proficiency instead. This has not caused problems at my own tables, and means people don't have to worry about exactly what features are granting them what proficiencies. The main reason I do this is because I believe getting a useless feature is unfun and arguably bad design. The reason I do not give them doubled proficiency (expertise) is because I believe these should be left to the Rogue and Bard classes; skills are a lot of their entire thing/kit.
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