Dear Querist,
Provisions of making pre-deposit (while filing appeals with first appellate authority & tribunal) were there in erstwhile excise & service tax regime as well since year 2014 / 2015. And, prescribed pre-deposit was made while filing appeal, there was always stay on balance demand (i.e. till appeal is disposed of).
And I do not see any confusion what-so-ever from reading of sub-section (6) & (7) of Section 107 and same is duly explained in earlier post of mine.
Over these years, I have filed hundreds of appeals for my clients (both in erstwhile regime & GST regime) after making prescribed pre-deposit. And Dept. NEVER sought separate application for stay for balance demand EVER.
W.r.t. appeal in special cases for Trans-1/2 matters emanating from the directions of the Hon’ble Supreme Court in the case of Union of India v/s Filco Trade Centre Pvt. Ltd., SLP(C) No.32709-32710/2018.- 2022 (7) TMI 1232 - SC ORDER), you must mention serial No. 3 of Notification No.29/23-CT dated 31.7.23 in your appeal memorandum itself (i.e. against re-deposit columns) explaining reasons for not making any pre-deposit. And, these procedures are binding on first appellate authority, being issued under Section 148 of the CGST Act, 2017.
If any objection is indeed raised at the time of / after filing of appeal (though I doubt it very much, when legal provisions are so clear), you can always educate concerned Dept. officer.
These are ex facie views of mine and the same should not be construed as professional advice/suggestion.