I know using one address is not recommendable but just for the sake of knowing, if using one address for the many input with few or far less output, can it still lead to increase transactions fee?
Yes. Transactions consists of scripts and the outputs defines the requirements needed to spend the UTXOs. For each transaction, there is a script that fulfills the requirement to spend the UTXOs (inputs).
That being said, within a transaction, for each UTXO, the script will define the public key and signature for
each and every input. This means that it doesn't matter if you're spending from different addresses because the size of each individual inputs will be the same. The only thing that affects the size is the type of transaction and the number of inputs and outputs.