Short answer-this will not create any issue, provided your value and tax reporting are correct.
Under GST law, for services (SAC), "quantity" is not a relevant or mandatory parameter. The schema for e-invoicing permits a default quantity (often "1") merely for system validation, since every line item requires a numeric field. That is why software like HostBooks auto-populates Qty = 1.
On the GST return side (GSTR-1), once you select an SAC, the quantity field is intentionally disabled, because services are not reported in terms of physical units. The law and return format focus on taxable value, rate, and tax amount, not quantity.
There is therefore no inconsistency in law between:
From a compliance perspective:
The Invoice Reference Number (IRN), taxable value, and tax amounts are the critical matching parameters.
Quantity is not used for reconciliation between e-invoice data and GST returns for services.
Risk view:
No adverse consequence should arise merely due to this difference. This is a known system behavior across ERPs and is accepted in practice.
Practical safeguard:
Ensure that:
Description of service, taxable value, and tax are correctly reported, and
There is consistency between books, e-invoices, and GSTR-1.
As long as these are aligned, the presence of "1" as quantity in e-invoices for services will not trigger any future dispute or mismatch.