The super yoctoish way would be to alter the packaging of the recipe to your needs.

Let's assume recipe-a consists of the files

foo
bar

and it would package both files into recipe-a pkg.

In the actual image you only install packages into a file system, so if you don't want bar to be installed into your final image, it'd be best to package bar into a separate package.

PACKAGES_BEFORE_PN = "${PN}-bar"
FILES:${PN}-bar = "bar"

in this case the recipe would produce

recipe-a (containing just foo)
recipe-a-bar (containing just bar)

You could install now (via IMAGE_INSTALL in your image recipe) just add recipe-a and only foo would be put into the final image.

While a potential other image (IMAGE_INSTALL += "recipe-a-bar recipe-a")
would contain both.

But if you'd go down that road you have to make sure that runtime dependencies between the packages are met (using REDEPENDS:* statements), as otherwise it could turn into very hard to debug issues.
So I would propose to **not** do that via bbappends, but forks of the recipes you want to repackage.

Another option (as likely mentioned already) is to use

rem_stuff() {
rm ${IMAGE_ROOTFS}/<file you want to delete>
}

ROOTFS_POSTPROCESS_COMMAND += "rem_stuff;"

in your image recipe