If consumption tax paid is smaller than consumption tax received, there is consumption tax payment to tax authority rather than refund as long as it is under consumption tax payer status. It is bit more complicated to drive consumption tax amount, but just simple idea is A. Consumption Tax received (National ; Local) – B. Consumption Tax paid (National ; Local) = Balance for payment or refund (=A-B)
In the case of consumption tax, without PE, it is possible to charge and be charged as long as the transaction is handled in Japanese market. And a company needs to appoint any local tax agent because there is no PE in Japan. The company appoint it when they are becoming tax payer for consumption tax to do payment and claim refund process to tax authorities on behalf of themselves. In the case of a company (with no PE in Japan), the 1st start FY is counted for the date when they start doing business with Japan market (but follow their own FY period) and the Tax payable revenue is counted for the amount in relation to only Japan market. (But, there is PE risk as well)