Yea, I ran into the same issue. It's not storing the formatted markdown but rather using the intermediate grid state. So markdown is always regenerated rather than edited in place. Basically, it just recalculate column widths and regenerate the pipes and padding each time. Alignment is stored separately (parsed from the separator row on import), so it’s reapplied when generating the markdown.
My co-worker and I were chatting about having all the online markdown editors looking like a wordpad and not excel, so in attempt I tried Google Antigravity for the first time, and built a small web app that behaves more like Excel for tables. It’s open source on GitHub in case anyone finds it useful. Feedbacks are welcome!