You don't have to use autotools, but it makes doing the right thing easy. If you want to use CMake (I much prefer it myself!) just make sure you use pkg-config, same with scons or whatever. These are all included in Fedora's (my distro of choice) package collection and there's no trouble using them to build.

But please, if you decide to bundle third party libraries make sure you can build without them and use ones provided by the system instead. It's a political nightmare to include packages with bundled libraries because it makes security updates a huge headache since we can't simply rely on Anitya (https://release-monitoring.org/distro/Fedora/) to send us notifications that a new release of the library is available, not to mention the extra work of actually updating the bundled library once we do find out an update has been published.

It is best to not bundle third party libraries, instead, have your build system check if the libs are installed and if they aren't then download and build them. rleigh mentions below that cmake can do that.

It absolutely does not make it worse for general users in the process. The whole point is to help the user! I'm not saying there aren't problems on the distro side. Distributions like Debian do have the problem of moving much too slowly, and apt and the other "imperative" package managers are severely flawed, but the basic best practices I aligned make things better for all users.

And I'm not saying that you should never provide some prebuilt binary to your users if their distro is lagging behind. And if you really feel the need to bundle third-party libs then just make sure there are configure switches that can be flipped so that system libs are used instead. The best thing for users is for them to be able to get all of their software from their distro, and that requires distros and upstreams to each do their part.