A solution is available, with a updated copy of tmux, and a recipe, see:

http://github.com/tmux/tmux/issues/2636#issuecomment-817542083

** Bug watch added: github.com/tmux/tmux/issues #2636
   https://github.com/tmux/tmux/issues/2636

** Description changed:

  choose-window produces a sensibly aligned list
  on centos7 (tmux-1.8-4.el7.x86_64):
  (0)  0: htop  "umari"
  (1)  1: bash  "umari"
  (2)  2: bash- "umari"
  (3)  3: bash* "umari"
  
  and ubuntu xenial (tmux 2.1-3build1):
  (0)  0: [tmux]- "jocur"
  (1)  1: bash* "jocur"
  
  but more recent versions produce an annoyingly misaligned list due to the new 
session line:
  (0)  - 0: 4 windows (attached)
  (1)  ├─> 0: man- (1 panes) "e540"
  (2)  ├─> 1: bash (1 panes) "e540"
  (3)  ├─> 2: ssh* (1 panes) "e540"
  (4)  ├─> 3: bash (1 panes) "e540"
  
  so when you choose a window from the new choose-window list, you have to
  look carefully and choose "the wrong window" or you get the wrong
  window!  is there a way to fix or workaround this problem?
  
  because this shows 0 on windows other than window 2:
  $ tmux bi w choose-t -wF'#{==:#{window_index},2}'
  (0)  - 0: 1
  (1)  ├─> 0: 0
  (2)  ├─> 1: 0
  (3)  ├─> 2: 1
  (4)  ├─> 3: 0
  
  thus this eliminates windows other than window 2:
  $ tmux bi w choose-t -wf'#{==:#{window_index},2}'
  (0)  - 0: 6 windows (attached)
  (1)  └─> 2: ssh* (1 panes) "e540"
  
  so similarly since this shows 0 on the session line and 1 on each window:
  $ tmux bi w choose-t -wF'#{window_format}'
  (0)  - 0: 0
  (1)  ├─> 0: 1
  (2)  ├─> 1: 1
  (3)  ├─> 2: 1
  (4)  ├─> 3: 1
  
  you'd expect this to eliminate the session line, and restore proper alignment 
of the choose-window listing, but strangely it just doesn't:
  $ tmux bi w choose-t -wf'#{window_format}'
  (0)  - 0: 4 windows (attached)
  (1)  ├─> 0: man- (1 panes) "e540"
  (2)  ├─> 1: bash (1 panes) "e540"
  (3)  ├─> 2: ssh* (1 panes) "e540"
  (4)  ├─> 3: bash (1 panes) "e540"
  
  so a fix or workaround would be greatly appreciated!
  
+ A solution is available, see:
+ https://bugs.launchpad.net/ubuntu/+source/tmux/+bug/1891785/comments/7
+ 
  ProblemType: Bug
  DistroRelease: Ubuntu 20.04
  Package: tmux 3.0a-2
  ProcVersionSignature: Ubuntu 5.4.0-42.46-generic 5.4.44
  Uname: Linux 5.4.0-42-generic x86_64
  ApportVersion: 2.20.11-0ubuntu27.4
  Architecture: amd64
  CasperMD5CheckResult: skip
  Date: Sat Aug 15 21:05:07 2020
  InstallationDate: Installed on 2020-03-15 (153 days ago)
  InstallationMedia: Lubuntu 20.04 LTS "Focal Fossa" - Alpha amd64 (20200314)
  ProcEnviron:
   LC_TIME=en_DK.utf8
   TERM=screen
   PATH=(custom, no user)
   LANG=en_US.utf8
   SHELL=/bin/bash
  SourcePackage: tmux
  UpgradeStatus: No upgrade log present (probably fresh install)

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https://bugs.launchpad.net/bugs/1891785

Title:
  choose-w misaligned (regression)

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