I've compiled Emacs 26.0.90 and made the same experiment.
I can confirm that it is fixed.
(I.e., the values I tried to either via "smie-config-set-indent" command or by editing ~/.emacs file are no longer ignored.)

Thank you very much.

On 11/23/17 20:26, Stefan Monnier wrote:
> forcemerge 24848 29414
> thanks
> 
>> - I run the following command:
>>
>>     M-: (print smie-config)
>>
>>   I see
>>
>>     ((tuareg-mode (4 :before "|-or" nil)))
>>     ((tuareg-mode (4 :before "|-or" nil)))
>>
>>   I have no idea whether this an expected or unexpected value. :-/
> 
> Yes, it's expected because M-: already prints the result of the
> evaluation, and `print` returns its argument.  IOW better just use
> M-: smie-config RET
> 
>> - Now my ~/.emacs file looks like this:
> [...]
>>      '(smie-config (quote ((tuareg-mode (4 :before "|-or" nil))))))
> 
> Looks good.
> 
>> - I press TAB.
>>   What I see is that the whole line is shifted to the right by 2 columns.
> 
> Which is what happens by default, so it shows that the setting didn't
> take effect.  I tracked this down and this happens to be a known bug
> which was recently fixed in smie.el.  More specifically, it
> should be fixed in the current Emacs-26 pretest.
> 
> I reproduced the corresponding patch below,
> 
> 
>         Stefan
> 
> 
> commit a58d0c590a777be98e58cd8c92ee1381e07e9b2d
> Author: Noam Postavsky <npostavs@gmail.com>
> Date:   Wed Aug 30 19:31:48 2017 -0400
> 
>     Fix loading of smie-config rules (Bug#24848)
>     
>     * lisp/emacs-lisp/smie.el (smie-config--setter): Use `set-default'
>     instead of `setq-default'.
>     (smie-config): Use `custom-initialize-set' instead of
>     `custom-initialize-default' as the :initialize argument.
>     
> diff --git a/lisp/emacs-lisp/smie.el b/lisp/emacs-lisp/smie.el
> index 87c4782e21..da1e12b140 100644
> --- a/lisp/emacs-lisp/smie.el
> +++ b/lisp/emacs-lisp/smie.el
> @@ -1956,7 +1956,7 @@ smie-config--mode-hook
>  (defvar smie-config--modefuns nil)
>  
>  (defun smie-config--setter (var value)
> -  (setq-default var value)
> +  (set-default var value)
>    (let ((old-modefuns smie-config--modefuns))
>      (setq smie-config--modefuns nil)
>      (pcase-dolist (`(,mode . ,rules) value)
> @@ -1982,7 +1982,7 @@ smie-config
>    ;; FIXME improve value-type.
>    :type '(choice (const nil)
>                   (alist :key-type symbol))
> -  :initialize 'custom-initialize-default
> +  :initialize 'custom-initialize-set
>    :set #'smie-config--setter)
>  
>  (defun smie-config-local (rules)
>