Take California for instance:

If a qualified political party chooses to hold a modified-closed presidential primary, the party must notify the California Secretary of State no later than the 135th day before Election Day.

https://www.sos.ca.gov/elections/primary-elections-california

That is a deadline that was within days of passing. Do you think it's better to just not have your candidate show up on the ballot??

The way they run the primers is entirely up to them

Stop spreading misinformation just because it feels right. No it is not. That is just one deadline for one type of primary in one state. There are 50 different sets of regulations and deadlines for each state. You cannot believe your own bullshit at this point