In that case, it may be just as easy to start right off the bat using StructureMap or AutoFac instead of the limited built-in provider. If you are writing a console app, then you likely don't need MVC or other ASP.NET Core specific services. If you later add a third-party container, those dependencies are passed across to be re-registered, so they are available when resolved via the third-party. When you call the AddMvc() extension method in your Startup.ConfigureServices method, the framework registers a whole plethora of services with the container.
One of the advantage of the built-in container in ASP.NET Core is that the framework libraries themselves register their dependencies with it. Having said that, whether it is worth using in this case is another question. NET Core console application? The short answer is not out-of-the-box, but adding it in is pretty simple. One question that's come up a few times, is whether you can use the built-in provider in a. Luckily, third party container are pretty easy to integrate, and are going to be getting easier. For small projects it may be fine, but if you need convention based registration, logging/debugging tools, or more esoteric approaches like property injection, then you'll need to look elsewhere.
Whether you choose to use the built in container or a third party container will likely come down to whether the built in container is powerful enough for your given project. There may be various disagreements on the way that is implemented, but in general encouraging a good practice by default seems like a win to me. One of the key features of ASP.NET Core is baked in dependency injection.