FWIW, I was able to correct the integration issue by editing the /includes/modules/pages/checkout_payment/jscript_square.php (it's also copied to the /checkout_one/jscript_square.php for the OPC integration) and changing:
Code:
if ($payment_modules->in_special_checkout()) {
return false;
}
to
Code:
if ($payment_modules->in_special_checkout() || (isset($payment_modules->paymentClass) && $payment_modules->paymentClass->code != 'square')) {
return false;
}
The result is that Square's jQuery module doesn't load if the payment class is selected and it's not Square.
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