I use the plugin “WordPress MU Domain Mapping” for mapping domains to subfoldered-subsites. Works well (even though it hasn’t been updated in 2 years), once you closely follow the instructions.
Available here: https://wordpress.org/plugins/wordpress-mu-domain-mapping/ .
(Although, on retrospect, this may not entirely be the answer to the OP’s question; I may have misunderstood his intent.)
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