I think that the bonus function is there to allow investors to invest more than their regular tsumitate instalments when they get paid their (usually) twice yearly bonuses.
So it's basically tough cheese, if are unable to invest up to the annual quota due to starting the tsumitate part way through the year, is what I assume the FSA and SBI people decided when they decided they needed to patch the loophole in the system which allowed some users to invest the maximum quota amount in one single month, rather than taking the tsumitate route.
That's what I understood from the below bit in the SBI announcement:
本サービスでは、定期的な積立の設定金額にかかわらず、つみたて投資枠の年間投資上限である120万円までの追加買付設定を受付けております。 このたび、長期・積立・分散投資による資産形成を後押しする制度の趣旨に鑑み、2025年1月(予定)に以下のとおり「ボーナス月の積立設定」の上限金額を引き下げる仕様変更を実施いたします。
In consideration of the purpose of the system to support asset formation through long-term, distributed, and diversified investment, we will implement a specification change in January 2025 (scheduled) to lower the upper limit of the "bonus month savings setting" as follows.