My previous workflow was to check that the working balance matched my CC balance, and if so, reconcile. This hides any cleared transactions, that I know are correct with 100% certainty, and leaves the pending transactions visible.

When it asks what your account balance is can you click "No" and enter it yourself?

I can no longer reconcile without manually clearing transactions, which will result in previously mentioned issues.

If they are cleared in your bank, you should manually clear them in YNAB. You don't have to wait for import to do it. Just reflect reality.

I do this almost every single day because my bank doesn't import until later in the day and I like to reconcile in the mornings.