Added (manually) to commit tagged emacs-26.1.92, in defcustom auto-save-list-file-prefix':

  :initialize 'custom-initialize-delay

Done same tests with auto-save configuration commented out in "please-do-it.el". 

- The directory .emacs.d is created

- It is populated with a directory auto-save-list-file-prefix

Checked that emacs is actually the one I've just build: it is.

Also checked that /usr/share/emacs/26.1.92/lisp/startup.el* are up to date: they are, though sibling .el are not affected except subdirs.el.

Thus, no, it does not seem to work.

Shall I try from another commit ?

De: "Eli Zaretskii" <eliz@gnu.org>
À: "bruno vasselle" <bruno.vasselle@laposte.net>
Cc: 37116@debbugs.gnu.org
Envoyé: Mardi 20 Août 2019 18:55:50
Objet: Re: bug#37116: 26.1; User choice user-emacs-directory is not honored
> Date: Tue, 20 Aug 2019 16:33:46 +0200 (CEST)
> From: bruno.vasselle--- via "Bug reports for GNU Emacs,
>  the Swiss army knife of text editors" <bug-gnu-emacs@gnu.org>
>
> Alright... but it's not legitimate: as I've set `user-emacs-directory', I should not have to furthermore tell
> auto-save where to put its material. If I need to, this means I need to also for every possible package that uses
> user-emacs-directory. And emacs still trashes my home directory.
Does the patch below solve your problem?
diff --git a/lisp/startup.el b/lisp/startup.el
index 32051c2..d753e6a 100644
--- a/lisp/startup.el
+++ b/lisp/startup.el
@@ -405,6 +405,7 @@ auto-save-list-file-prefix
 Directories in the prefix will be created if necessary.
 Set this to nil if you want to prevent `auto-save-list-file-name'
 from being initialized."
+  :initialize 'custom-initialize-delay
   :type '(choice (const :tag "Don't record a session's auto save list" nil)
                  string)
   :group 'auto-save)