Techniques are described for facilitating execution of software programs in a configurable manner, including to configure bootstrapping operations that are performed at startup of the software programs. At least some of the software programs may be software images that each include, for example, a defined file system, an operating system, and one or more application programs. In addition, configuration of the software programs' startup may include using distinct bootstrap packages that each include their own distinct file system, such that loading of a bootstrap package within a software image includes adding the included file system of the bootstrap package to a new location within the defined file system of the software image (e.g., by mounting the included file system of the bootstrap package within the defined file system of the software image, and optionally removing the included file system of the bootstrap package after bootstrapping operations are completed).