Apple ID - Two Factor Authentication (and why I stopped using it)

The Apple devices I use every day consist of the following:
2009 MacBook Pro 17" (home)
iPhone 6 (home)
2012 MacBook Pro Retina (work)
My home devices are all logged in using my Apple ID as usual, and my work laptop uses a Apple ID specific to work, but with my personal Apple ID logged in for iMessage and FaceTime (pretty standard, I presume, for people with full-time work laptops they can bring home, etc.). Now, since I have multiple devices which are constantly syncing everything back and forth, whether it be something as simple as my contacts or as delicate and near and dear to my heart as my photo collection, I felt that maybe I should use two factor authentication for my home Apple ID, just to be on the safe side. I recognize that the two factor authentication only protects iMessage and FaceTime currently, but I implemented it with hopes that someday they will incorporate everything about iCloud and other services synced between Apple devices that you would assume should be covered by a two factor authentication update/overhaul.
I liked this idea very much, as I use two factor for almost everything I can, but things started to fall apart one day when I had to switch to a temporary work laptop and decided to log in to iMessage with a new app specific password, as you would need to on a new device (unless you wrote down the original iMessage password, which is a terrible thing to do). When I went to create my new iMessage password for work laptop B, I decided to revoke work laptop A's iMessage password while it went in for repairs. This wasn't so bad until something seemed funny about my phone, as it was asking for me to log into iMessage again. Now, I had created a separate password for work laptop A's iMessage when I first logged in a while back, as well as a separate password for the temporary work laptop B so it didn't interfere with my other generated passwords. Apparently this didn't matter.
I continued and created a new app password for my phone, but when I got home, wouldn't you know it, I had to log into iMessage on my home laptop again as well. I had to create a new password for that, which seemed to work for a while, but then I was prompted to enter my iMessage password on my phone again once I revoked my home laptop's iMessage password. Not following? No, me either. It seemed to me that creating separate app specific passwords for me to use across my devices didn't stay as separate as I thought they should, but instead they somehow seemed to be dependent on one another. Since I had a frustrating time trying to activate iMessage again on my iPhone and laptops on multiple occasions while this was happening, I decided to disable two factor authentication altogether.
I suppose I should ask a question here, so here goes: has anyone else encountered this horrific two factor authentication/app specific password management issue for their own account? Have you been able to resolve it, and if so, any helpful suggestions? Thanks!

I had also thought that initially, but after turning it on, I went to sign into iMessage with my Apple ID and regular Apple ID password, but it prompted me to create an app specific password to sign in since I had two factor authentication on, as it wouldn't let me use my regular Apple ID password to log in (which I could use to log in for everything else but iMessage and FaceTime). It was nice since I was prompted to provide a code sent to an Apple device of my choosing when signing into the Apple ID management site or iCloud.com, but forcing me to create app specific passwords for iMessage and FaceTime is kind of ridiculous and frustrating. Maybe there's a way to have two factor authentication without the need for app specific passwords? Or if not, then perhaps that would be a great option to present users when turning that feature on.

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