Different Single as homepage for other languages
You don't need to use the "This is for the homepage" checkbox at all. All it does is to (1) set up
a route to the entry template specified in the section settings and (2) make the entry model available to this template
from an entry variable.

You can just deselect this option and configure the above manually. The simplest way to set up a route for the homepage is
to create a template index.html in craft/templates/ and Craft picks it up automatically for hompage requests (→ see pt. 6 in the routing docs).

You can now query for the entry model (your "single") depending on the requested locale to solve (2) and then include a template partial
into the index.html to solve (1).

{% if craft.locale == 'fr' %}
    {% set entry = craft.entries.section('home_fr').first() %}
    {% include '_pages/home_fr' %}
{% elseif craft.locale == 'de' %}
    {% set entry = craft.entries.section('home_de').first() %}
    {% include '_pages/home_de' %}
{% else %}
    {% set entry = craft.entries.section('home').first() %}
    {% include '_pages/home' %}
{% endif %}