"I could pay penalties if I am correct?" - yes
"Is it possible to pay the owe that is not shown on IRS yet through direct pay online before file the 1040x to pay on time" - I would try that. Your payment should go into your account and wait for the 1040X. Of course, in these times, it's a bit difficult to say how things will be handled at the IRS in any specific case, but I don't believe the IRS ever complains about receiving too much money. And by the time they might decide to send it back, hopefully, they will have processed your 1040X and realized why you sent it.
"I have to send with a check and wait until they notice the file" - No, don't wait, pay now. Cut off any potential interest and penalties.
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