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Currently, the Portuguese localization uses a space as the thousands separator character ({{formatnum:999999999.99}} = 999 999 999,99).

Per discussion at
[[pt:Wikipédia:Esplanada/propostas/Usar espaço não-separável como separador de milhar (3abr2012)]]
it should be used a non-breaking space ( ) as the thousands separator mark in Portuguese.

Therefore, please update the $separatorTransformTable to
$separatorTransformTable = array( ',' => "\xc2\xa0", '.' => ',' );