在香港註冊的有限公司

No. It is quite frequent in Hong Kong for this kind of arrangement.
The payment and receipt of fund is only a fund transfer. This has no implication to the substance and the nature of trade business carried out by this Hong Kong company and thus has, in principle, no tax problem. It is a matter of authorisation that you have to receive from the supplier in mainland that the payment to a named party from him constituted a full settlement of the balance due to this supplier. There will be no more legal obligation of the company to the supplier after the said payment. Moreover, the payment is a genuine payment to the bank account of that named person and is reflected in your bank account statement.

公司在平常的營運下，當然無人理會你付款給什麼人，但實際上每一筆交易都應該要有得解釋的，因為你報稅後稅局隨時有權要求你這樣做，如果不能解釋隨時會懷疑你瞞稅。
以你的情況，由於國內的公司和你公司有交易關係，所以你付款給這間公司當然是可以解釋的，但如果對方要求你存款入某個香港戶口，表面上這個收款人與這單交易沒有關係，但其實做法可以很簡單，你只需要求那間國內公司向你發出一份書面的支付訂金通知書，文件內寫明這單交易的資料，及對方要求你將這批貨的訂金存入某個指定的香港戶口，這樣的話那個收款人便與這單交易有關了，而你這筆付款便可以有充份解釋了。