Is it necessary to run with the command bootstrap=true for upgrading form 10-11 and/or 11-12, or can the scripts be just run manually instead?
You need to have bootstrap=true. The base system as well as any plugins will use the bootstrap mechanism to perform any changes needed for the upgrade. It is not feasible to do this manually.
Being that necessary, it’s ok if there is no propagation of configuration to the target environment, right?
For example, if in the code of the project, in the bootstrap module they have specific hosts, bootstrap should be enabled but in hippoecm-extension.xml it wouldn’t be necessary to flag the host group as exportable to the environment.
below I’ve included some documentation links for reference. You configuration contained in your project will be loaded once if referenced in the hippoecm-extension.xml. In order to reload it it needs a version number and a reloadonstartup=true element. Depending on how you configured it your bootstrapped hosts may be applied to other environments, but generally this should not matter much anyway. Presumably the hosts you configure locally or for a specific env are different from those of any group. It is quite common to keep all host configuration from all servers in the bootstrap content.