The important factor for me that cuts strongly towards this being an equipment and staffing issue was the abrupt resumption of daily long distance service.
During the modified schedule (and correct me if I'm wrong) most trains still had their full consists. Staff were furloughed as there were less weekly trains, and cars were put into storage. But the actual consists were the same size on the days the train still ran.
Hoping into the time machine to late winter/early spring, the Biden stimulus and congressional mandate to resume service happened very quickly. Even the existence of the third stimulus package was in doubt up until the Senate special elections in December of 2020.
If your staff has been furloughed and cannot be 100% recalled, and your cars are in storage, the only way to resume daily service asap is to run the consists shortened. It takes more time to come out of a furlough/service reduction that it does to go into one. And it certainly takes longer than the lead time given to Amtrak by Congress.
All of that is to say, the likeliest, and simplest, explanation, is that Amtrak was unprepared to resume full daily service, and did not have the staff or rolling stock to do so without cutting consist size.