"1) Would a commercial enginge available for Indies (up to 5000$) allow this level of costumization"
No. You're going to have scalability issues. Why? Because most extant MMOs (and hence their engines) are based around rather static world geometry. Minecraft keeps the geometry local and generates by psuedorandom techniques when required, saving the areas as it does so.
In order that you can have a landscape like that but which can be altered by any of the players, you'll need to store the whole landscape (in the way Minecraft does) but also to send deltas in that landscape to all players who can see the change (and you'll need to determine who can see each change). In addition you not only have to tell players connected now about changed geometry, you'll need to tell all the players who will reconnect later about changes.
It's not impossible, but it's a difficult problem to solve well. Which brings me onto the next part...
" If nothing of the above works for me then I would have to build it, with something like Boost as you suggested, nfries88. How long would that take me, providing I can work lets say the average 40 hours a week in the project. 1 year? 5 years? 10 years? (I can't spend more time than that"
If you are at the stage of referring to Boost as "something like Boost" then you have a number of things ahead of you.
You need to;
1. Get good at C++.
2. Get good at games development.
3. Write this game.
There's a reason why, when I go shopping for good C++ developers, I'm looking for people who've been using it for several years. It takes of the order of 10000 hours to get good at something. There are about 2000 working hours in the year, so 5 years is the point at which people could be good. 5 years does not MAKE a good C++ developer[2] but the chances of someone with a year of it being good are so small it's not worth worrying about. It's not that I wouldn't hire them, but I would be aware that if I hire them I'd be expecting to have a lot of conversations about segfaults.[1]
Games dev is a related but different set of skills. It's about understanding how to handle game loops, to defer doing things, to cache things, to handle inputs in the right way, to look at a set of problems and understand how to solve them not just in performant ways but within the envelopes of games. To understand things like "good enough is good enough", "faking it is cheaper than doing it" and "neither you nor the player needs this". These are skills which also need honing. They're less technical than the development -- they're about psychology, project scope management, product ownership and control. But they still need to be learned and practiced.
I'm telling you all this because "1 year is a fair estimate for a basic Minecraft-like MMO. Certainly less than 5 years" is almost certainly untrue. It's not a malicious lie; it's an untruth born of optimism. But it's still unlikely to be true. And you'll be disappointed. Minecraft's a tricky problem to solve -- and to be clear here, Notch is NOT a beginner. It's not his first released game nor is it his first released bit of software. And it's taken him a year. And an MMO version of it is a step further on.
Why DOES everyone want to write an MMO as their first game? What happened to implementing things like Qix or Pong or Breakout so that you get the hang of the basic principles before leaping straight into client-server software that is complex by anyone's standards?
[1] Yes, I know everyone here is an EXPERT in C++, and that you all got that way in just a couple of weeks and that you're all exceptional in this. So don't even bother telling me.
[2] This is a common commercial error in hiring processes.
