I think we waited too long with training our puppy to be alone

To preface this, I'm not talking about leaving her alone for 8 hours, and she is also crate trained. I'm talking one minute alone so that I can pee.

We have a 12 week old working line German Shepherd, who we got when she was 8 weeks. For the first two weeks we allowed her to sleep outside a crate and gradually introduced the crate before eventually realising we had to just rip off the band aid and make her sleep in there.

She sleeps just outside our bedroom in the crate, and will often complain when we put her in there for 30 secones to a couple of minutes before settling and falling asleep. She takes naps in the crate during the day, and again, we might get a little toddler "I don't want to nap" whining (not barking or howling, just complaining) before she lays down.

We walk her twice a day, play tug and with a flirt pole 4 times a day, free play in the garden and 4-6 training sessions a day. We also make her work for all meals with a lick mat, slow feeder, puzzle feeder, or scattering her food to make her find it. If we're using something that fits in her crate for feeding, she eats in her crate. She puts her toys and chews in there herself and is fine going in and out on her own.

If I give her a frozen kong, I have even been able to take meetings for 30 minutes in another room with the door open with her in the crate (crate door closed). She will also go out for free play in our garden alone, and comes to check in every now and then.

We always have someone at home, and we basically never leave her alone. If my girlfriend and I go upstairs together she loses her mind, howling and barking. If my girlfriend is at work and I go to the bathroom without giving her a kong or something, she freaks out 30 seconds after we leave. We can't go to the store at the same time, and if she naps and one of us leaves the room she'll wake up and lose her shit too. I think we should have started leaving her earlier, as now she always expects at least one of us to be around. If she has a kong and hears the front door close, she loses interest and will start crying, even if another one of us is in the room. We don't make a big deal out of leaving, and try to keep things normal so as not to enforce anxiety. We give her treats when she's calm, similar to how we crate trained her.

How do we reverse this? Do we really need to start with 10 seconds and work our way up? It sounds like it could be months before we can go to the bathroom! Does anyone have any advice?