Bits of frame manipulation from my init.el to reproduce positioning issue

repro.el

;;; init.el --- load the full configuration -*- lexical-binding: t; -*-
;;; Commentary:
;;; Code:

(defconst my/screen-laptop (intern "my/screen-laptop")
  "Symbol to indicate display is MacBook Pro 16\" laptop screen.")

(defconst my/screen-4k (intern "my/screen-4k")
  "Symbol to indicate display is 4K screen.")

(defconst my/screen-laptop-4k (intern "my/screen-laptop-4k")
  "Symbol to indicate display width is laptop and 1 4K screen.")

(defconst my/screen-4k-4k (intern "my/screen-4k-4k")
  "Symbol to indicate display width is 2 4K screens.")

(defconst my/screen-laptop-4k-4k (intern "my/screen-laptop-4k-4k")
  "Symbol to indicate display width is laptop and 2 4K screens.")

(defconst my/screen-terminal (intern "my/screen-terminal")
  "Symbol to indicate display is a terminal.")

(defconst my/laptop-screen-width 2056
  "MacBook Pro 16\" M1 screen width in pixels.")

(defconst my/4k-screen-width 3840
  "4K external display width in pixels.")

(defun my/screen-layout ()
  "Identify current screen layout.
Uses result from `display-pixel-width' to determine what monitors
there are.  Better would be to use `display-monitor-attributes-list'
like done in `my/frame-top'.

Returns one of the follow symbols based on width:

- `my/screen-laptop' -- only laptop screen
- `my/screen-4k' -- only 4K monitor.
- `my/screen-laptop-4k' -- laptop screen + 4K monitor.
- `my/screen-4k-4k' -- two 4K monitors.
- `my/screen-laptop-4k-4k' -- laptop screen + 2 4K monitors.
- `my/screen-terminal' -- unknown screen."
  (declare (side-effect-free t))
  (let* ((width (display-pixel-width nil))
         (value (cond ((= width my/laptop-screen-width) my/screen-laptop)
                      ((= width my/4k-screen-width) my/screen-4k)
                      ((= width (+ my/laptop-screen-width my/4k-screen-width)) my/screen-laptop-4k)
                      ((= width (* my/4k-screen-width 2)) my/screen-4k-4k)
                      ((= width (+ my/laptop-screen-width (* 2 my/4k-screen-width))) my/screen-laptop-4k-4k)
                      (t my/screen-terminal))))
    (message "my/screen-layout: %s" value)
    value))

(defun my/is-laptop (layout)
  "T if LAYOUT is laptop."
  (declare (side-effect-free t))
  (eq layout my/screen-laptop))

(defun my/is-4k (layout)
  "T if LAYOUT is kind with at least 4K area."
  (declare (side-effect-free t))
  (memq layout '(my/screen-4k my/screen-laptop-4k my/screen-4k-4k my/screen-laptop-4k-4k)))

(defun my/rows (layout)
  "The number of rows to show in a frame shown on LAYOUT."
  (declare (side-effect-free t))
  (if (my/is-4k layout) 103 (if (my/is-laptop layout) 88 40)))

(defun my/cols (layout)
  "The number of columns to show in a frame shown on LAYOUT."
  (declare (side-effect-free t))
  (if (or (my/is-4k layout) (my/is-laptop layout)) 132 80))

(defun my/frame-pixel-width (layout)
  "Width in pixels of a normal frame shown on LAYOUT.
These values are hard-coded based on current settings.
Probably a better way to figure this out."
  (declare (side-effect-free t))
  (if (my/is-4k layout) 1338 944))

(defun my/frame-top ()
  "The top of the display area.
NOTE: this assumes that the laptop display, if present,
is on the left of any monitors."
  (declare (side-effect-free t))
  (let* ((settings (display-monitor-attributes-list))
         (top (nth 2 (if (eq (length settings) 1)
                         (car (car settings))
                       (car (car (cdr settings)))))))
    ;; (setq top -1267)
    ;; (setq top 0)
    (message "top: %d" top)
    top))

(defun my/frame-initial-left (layout)
  "Pixels to use for the `left' of a frame on LAYOUT.
This is to be used for the `initial-frame-alist' configuration."
  (declare (side-effect-free t))
  ;; Use the first external monitor if there is one.
  (if (memq layout '(my/screen-laptop-4k my/screen-laptop-4k-4k))
      2056
    0))

(defun my/initial-frame-alist (layout)
  "Make alist to use for the initial frame on LAYOUT.
Frame's left side is flush with the left side of the main display."
  (declare (side-effect-free t))
  (list (cons 'width (my/cols layout))
        (cons 'height (my/rows layout))
        (cons 'top (my/frame-top))
        (cons 'left (my/frame-initial-left layout))))

(defun my/frame-default-left (layout)
  "Pixels to use for the `left' of a frame on LAYOUT.
This is to be use for the `default-frame-aliat' configuration."
  (declare (side-effect-free t))
  (+ (my/frame-initial-left layout) (my/frame-pixel-width layout)))

(defun my/default-frame-alist (layout)
  "Make alist to use for the default frame on LAYOUT.
Frame's left side is next to the right side of the initial frame."
  (declare (side-effect-free t))
  (list (cons 'width (my/cols layout))
        (cons 'height (my/rows layout))
        (cons 'top (my/frame-top))
        (cons 'left (my/frame-default-left layout))))

(defun my/update-screen-frame-alists (layout)
  "Update frame alists for current LAYOUT."
  (modify-all-frames-parameters (list (cons 'top (my/frame-top))))
  (setq initial-frame-alist (my/initial-frame-alist layout))
  (message "initial-frame: %s" initial-frame-alist)
  (message "default-frame: %s" default-frame-alist))

(defun my/screen-layout-changed ()
  "Recalculate values based on screen layout."
  (interactive)
  (let ((layout (my/screen-layout)))
    (message "screen layout: %s" layout)
    (my/update-screen-frame-alists layout)))

(my/screen-layout-changed)

(provide 'repro)

;;; repro.el ends here.

Save above to ~/repro.el and then start Emacs from shell:

% /Applications/Emacs.app/Contents/MacOS/Emacs -Q -l ~/repro

Play with my/frame-top to adjust vertical positioning.