Base align is one of the options for default alignment that is found under coaching adjustments, in-game. I'm almost certain you can edit this from the main menu to have a default setting in all modes.
The choices are default, man, and base. Base puts everyone in a predetermined spot on the field. They do not react to offensive alignment at all. I use default which has a ton of overlap with man alignment. Man alignment will do things like send all your CBs to the 3 WR side against formations like Trey Y-Flex. Since I'm not crazy enough to leave LBs or Ss on an island against most TEs I just use default and it works fine. The trade off for me is that my weak side LB is going to have a ton of ground to cover from his quarter flat and the 3 rec gets stressed like crazy this year due to how cumbersome COD is for LBs. Get the best athletes you can on the field in these spots even if they are safeties.
Any benefit you get from base alignment can be achieved by manually moving your safeties presnap. You should be doing this on almost every down. Most defenses have them 15 yards off at the snap and this is too much cushion.
Deep posts should only be giving you problems when they are coming from isolated receivers. The FS is supposed to help on the in-cut but the transition didn't always animate well in the past 2 games. I haven't seen this issue at all playing M21, but it could still be there. You can either user the safety to smooth the transition or call one of Cover 6 or Cover 9, whichever option has the post running toward your deep half zone. The deep half will match the post. If you are getting beaten by deep posts from anywhere else you have match up problems. Move guys or start calling different defenses.
The best call against crossers is Palms. Even if it's a double crosser the AI should match one and you can take the other from the 3-rec. You cannot hesitate at all at the mesh point or you are toast. Practice, practice, practice both to get the stick work down and to hone your own play recognition. You must be able to anticipate when you need to switch and when you don't.
Since you are the 3-rec hook you always stay with number 3 (by outside-in count) and you will pass receivers off for one switch only. One of the best reasons to user this position always is that it's rule are by far the simplest and you can just play and not worry TOO much about your AI teammates unless the opponent really knows what they are doing. Crafty opponents can use hot routes and motions to manipulate your assignment. If you zig when you should've zagged it's a big play and 6 a high % of the time because RAC is easy.
If they are really killing you with deep digs I would play off man against them if at all possible. If it's coming from an isolated receiver you are free to switch him to man coverage from Palms without changing anything for anyone else on the field. You can also bring that FS a little lower into the box so he can insert himself into the play instead of dropping too far back.
Deep outs can get jumped by good man CBs this year, so that's an option. If you want to play zone and you really need to stop an out I would call Cover 2 Sink or split-field play and have the flat zone to the side you are worried about. I would also probably have flat zone depth set to at least 15 yards. If they had deep corners at their disposal I'd go 25 to be safe.
If you set flat zone depth and call Cover 6 or Cover 9 match principles are canceled so you must account for the fact you are playing spot drop cover 4. This need not be a bad thing if you don't over use it. Just bring guys into the box.
Your quarter flat zones should be keeping the flats secure. You won't lock them down, but you should be able to contain them and occasionally get TFLs and maybe even AI picks on good dice rolls if you have good players.
With sound route concepts your man can be taken out of the play so be mindful anytime your opponent completes one to the flat and he's nowhere to be found. You have a scheme problem that must be addressed! Screens can be a real issue if you get stuck on a DL or just get careless with your user.
If they are clearing out your clouds and hitting the flats under them (any play) then you also have a scheme problem. If you have flat depth on you can still get players to jump the flats by setting curl flat depth appropriately (0-5 yards) and hot routing.
I'm not messing too much with zone depth so far. I've stayed in match and my D still plays well enough that I've been competitive in all my H2H so far even though I'm giving up way more yards and points than last year. Offense is much easier this year.