Not at all. Handling different input styles (mouse vs touch), while not trivial, is a tiny fraction of the other work listed above that goes into targeting multiple platforms. Unity/Unreal let you focus on just that tiny part that actually matters to your game.
> If you're only targeting PCs (and I think most Indies are)
This is also not remotely true. The current generation of consoles, in particular, have been huge for indies. The majority of the games released on them have been from indies. And if you're taking gamepad input, you don't really even have the input-mode speed bump when it comes to supporting multiple platforms at once. Probably the only concern you'd have to deal with is level-of-detail, but you'd have to do that for PC anyway, and the engines give you tools that assist with it.
That's assuming the game is appropriate for a given platform. A mouse-based game with a lot of very small click targets (such as SimCity 2000) would not be playable on a touchscreen. The game would have to be dramatically re-designed to the point where it's a different game entirely. At that point, the advantage of having a "build for Android" button is greatly diminished.
If you're only targeting PCs (and I think most Indies are) then a framework like SDL gets you most of the way there to having your game run on Mac/Windows/Linux. It also does so without any of the financial cost of a proprietary engine and keeps things very simple so you can focus on building exactly what your game needs.