Unfortunately, I fear that once that happens, modded content will be monetized in some way shape or form - I hope it's not the case, but I feel it's a legitimate fear, given the track record of the gaming industry.
I understand your fear here, but I still say it's unfounded. It's thinking too small. For Microsoft to do that, it would be a massive squandering of about $2 billion. The model they've repeatedly stated was their goal, and so far their actions back it, all point to this not happening.
It'd be like slaughtering your cash cow for a steak and cheese. The goal, and only way the investment pays off, is to keep making Minecraft as ubiquitous (not the rapper) as possible. I cannot envision a scenario where they don't understand this. And the only way that works is if they continue encouraging the modding community to keep it relevant.
It's as simple as math. Which makes you more money? Let's use fake, but easy numbers just to illustrate it.
Scenario A (the worst case scenario) : Let's pretend there's a base of 10,000,000 minecrafters. Let's say they fully fix up C++ Minecraft and slap a store on there that lets you buy time shortcuts, like 1000 iron ingots for $0.99 or a diamond pickaxe for $1.99, whatever. This isn't a competitive game. It's not Clash of Clans or Heroes Charge where people feel compelled to spend all that money because their epeen is on the line. End result, lets say a 50% base growth over the next 10 years, with an average of $5 per subscriber in microtransactions (this is generous, IMO). That's 5 million new copies of the game, plus $5 per total sub: $100m + $75m = $175 gross (again, fake numbers for illustration, humor me).
Scenario B (the rosiest scenario) : This time, it's like it looks like already. They're regularly improving the game with free updates, but offering some (quality) texture packs, skins and worlds to download, while still allowing you to build your own. Eventually, the same scenario happens with a modding API. It's open for people to make whatever mods they want, as many as they want, forever. Inspired by some of these mods, they also develop their own custom game experiences once can add to their account for a small fee as well. They're already doing some of this now, only for free, but I'm projecting out scenarios in the future where they develop what would essentially be a full modpack, only professionally done, and charge, say $5 for it. Completely optional, and still doesn't bar anyone from creating or using anyone else's free packs.
Meanwhile, the value of the core product skyrockets. People continue catching on to the potential educational benefits of this kind of game and it becomes a standard essential purchase for every family. Every school system has it, using some third party mods to form the game for educational use. Every parent gets a license for every kid because it's a hell of a lot cheaper than Legos. This might have happened in the previous scenario, but while the world started to sour on the game, another company that "gets it" goes and makes a competing product tailor made for this. But in this scenario, it doesn't happen because there's already this huge, established and malleable core product, so everything gets tacked onto it.
So, now, lets say the average customer only spends $2 on extras. Enough to satisfy the digital stores it's on. But, instead of a 50% increase in the player base, it's a 300% increase over the next 10 years, with no signs of slowing down as it becomes an institution. 20,000,000 new fake customers, plus $2 per sub on extras = $400m + $60m = $460m over that same timespan.
Again, these numbers are made up for easy math*, but you can see how drastic the difference would be. The goal here is to continue to grow the player base, not to sap more money out of the ones that are there. This is KEY, and the only way the the $2 billion investment pays off.
Now, the reality will be a scenario C, where there's a bit of a mix in there, and this is Microsoft, so they'll make some mistakes along the way, I'm sure. But their eye will always be on scenario B.
*If anything, btw, these numbers are conservative. You wouldn't just have 20,000,000 new subscribers. You'd have these same people buying the game over again every time they get a new console. The player base could well be well over 30 million in 2027, too.
The microstransaction estimates are based on a free-to-play voxel game called robocraft that I used to play before I tried the real deal. It uses that kind of microtransaction model and even has the advantage of being a competitive game. The value you get for a few bucks is actually quite good and it has everything going for it. They make like and average of $2 per person. Optional cosmetic upgrades and time savers don't actually make that much money.
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