Update: I received confirmation from IRCC that they had received the receipt showing I had paid the fee difference three days after submitting via the webform. Fingers crossed that's the end of it...
Thank you for contacting Immigration, Refugees and Citizenship Canada (IRCC).
We are pleased to confirm the reception of the following document:
We have forwarded it and the information you provided to the responsible office for their consideration.
If further information is needed during the processing of your application, the responsible office may contact you.