You can replace the standard page meta by following a few simple steps.
For each of the modules that have detail pages, create two custom fields. Call them what you will so long as they are the same across all the modules, eg 'detail_keywords' and 'metadescription'.
At the end of your detail template, put:
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{assign var=metadescription value=$entry->fields.metadescription->value}
{assign var=detail_keywords value=$entry->fields.detail_keywords->value
This makes those vars available to the entire page, not just the individual modules.
Next, at the bottom of your page template, enter:
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{if !isset($metadescription)}{content block='metadescription' label='Page description for SEO' oneline='true'}{/if}
Next, in SEOTools2, wherever you have the {keywords} tag, say:
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{if isset($detail_keywords)}{$detail_keywords}{else}{keywords}{/if}
Although they only appear as single line fields, the SEOTools2 page title and meta title fields have full Smarty template processing capabilities.
Of course this will only work when the config process_whole_template is set to false. The body html must be processed before the head stuff.
Have fun with this,
psy