This is not a game design question. Moving it to an appropriate forum.

Keep in mind that 'indie' covers everyone from kids working out of their bedrooms in the weekends to industry veterans who have mortgaged their houses to fund a half-million dollar project, to indies who made ten million on their last project and are spending it all on their next one.

It's a very broad category of diverse situations...

For us: we made our own engine because it suited our situation. We were trying to make a physics-based high speed racer. We evaluated Unity (v3 IIRC), Unreal (3/UDK) and a bunch of less famous options. None would work for us out of the box - we would have had to rewrite the physics and networking parts of the engine for our game to work as we wanted. Plus they were all quite expensive at the time (Unreal3 wanted 25% of gross, compared to Unreal4's 5%!!). I had been working professionally as an engine programmer for about 5 years at the time, so I was almost capable of doing that job alone So we went down that path and made a very slim engine focussed only on the needs of our game (no general bloat / features we won't use). This has meant that we've spent a lot of time working on engine code instead of game code though. If we had been paying salaries to a team from the start, we would have gone bankrupt -- this plan only worked because we were all working for free/equity, making "wasting time" not so hurtful to the company. If we weren't indie (e.g. A publisher had thrown a million dollars at us back at the start), we probably would have had to license an engine so that we could start being productive immediately. 

Creating a game engine is usually the result of creating a game. It is fun but a lot of work. If I were developing games for a living, which I'm not, I would probably use Unity but then again I would look for an open source game like Mega Mario and use it's engine to develop my own game. However, developing a game engine allows you to learn about the inner workings of games but if you have to deliver on time don't do it and use something that was already made and make sure it have good documentation!