Reproduction with Emacs 29.3 (also with git master HEAD, see below).

Run: emacs -Q
C-x 5 2 ; window opens the same size as the initial window
M-x menu-bar-mode RET ; disable menu-bar-mode
C-x 52 ; window opens much smaller than initial window

With master HEAD (commit 92ea393a16e), the situation is slightly different:

Run: emacs -Q
C-x 52 ; window opens much smaller than initial window

When the new windows are opening at a small size, changing
default-frame-alist has no effect. When the new windows are opening at the
same size as the initial window (with Emacs 29.3, as above), then changing
default-frame-alist works as expected.

I'm running on Ubuntu 24.04, under GNOME 46 with X11. I don't have any
Emacs X resources set.

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