Confirmed.
Reproduced after the last update.
Intel HD 4000
Monitors:
VGA1 connected 1280x1024+1920+0
HDMI1 connected 1920x1080+0+0

According to xprop, the hints for the TF2 window are:

_NET_WM_STATE(ATOM) =
WM_STATE(WM_STATE):
window state: Normal
icon window: 0x0
_NET_WM_NAME(UTF8_STRING) = "Team Fortress 2 - OpenGL"
WM_NAME(STRING) = "Team Fortress 2 - OpenGL"
WM_PROTOCOLS(ATOM): protocols WM_DELETE_WINDOW, _NET_WM_PING
_NET_WM_WINDOW_TYPE(ATOM) = _NET_WM_WINDOW_TYPE_NORMAL
_NET_WM_PID(CARDINAL) = 22254
WM_LOCALE_NAME(STRING) = "C"
WM_CLASS(STRING) = "hl2_linux", "hl2_linux"
WM_HINTS(WM_HINTS):
Client accepts input or input focus: True
WM_NORMAL_HINTS(WM_SIZE_HINTS):
user specified location: 960, 560
program specified minimum size: 640 by 480
program specified maximum size: 640 by 480
WM_CLIENT_MACHINE(STRING) = "mauser"
_MOTIF_WM_HINTS(_MOTIF_WM_HINTS) = 0x2, 0x0, 0x1, 0x0, 0x0

This could be caused by WM_NORMAL_HINTS saying that the window has to be exactly 640x480. My configured resolution in TF2 is 2560x1600 fullscreen and I am using dwm as my window manager.

i'm found workaround:

Right-click TF2 in the STEAM browser.
Properties
Set Launch Options...
-windowed

Launch game, reconfigure to fullscreen mode... PROFIT

Fixed in the latest version of TF2.

Confirm, working now.

Hi, I am having this issue again. All Source 1 main games suffer from this issue, like TF2, HL2DM.

L4D branch derived games (L4D2, CS:GO, Dota 2) start in full-sized bordered window which is offset by the GNOME topbar.

Computer Information:
    Manufacturer:  Unknown
    Model:  Unknown
    Form Factor: Desktop
    No Touch Input Detected

Processor Information:
    CPU Vendor:  GenuineIntel
    CPU Brand:  Intel(R) Core(TM) i7-8700K CPU @ 3.70GHz
    CPU Family:  0x6
    CPU Model:  0x9e
    CPU Stepping:  0xa
    CPU Type:  0x0
    Speed:  4700 Mhz
    12 logical processors
    6 physical processors
    HyperThreading:  Supported
    FCMOV:  Supported
    SSE2:  Supported
    SSE3:  Supported
    SSSE3:  Supported
    SSE4a:  Unsupported
    SSE41:  Supported
    SSE42:  Supported
    AES:  Supported
    AVX:  Supported
    AVX2:  Unsupported
    AVX512F:  Unsupported
    AVX512PF:  Unsupported
    AVX512ER:  Unsupported
    AVX512CD:  Unsupported
    AVX512VNNI:  Unsupported
    SHA:  Unsupported
    CMPXCHG16B:  Supported
    LAHF/SAHF:  Supported
    PrefetchW:  Unsupported

Operating System Version:
    "Fedora release 33 (Thirty Three)" (64 bit)
    Kernel Name:  Linux
    Kernel Version:  5.9.8-200.fc33.x86_64
    X Server Vendor:  Fedora Project
    X Server Release:  12009000
    X Window Manager:  GNOME Shell
    Steam Runtime Version:  steam-runtime_0.20201104.0

Video Card:
    Driver:  NVIDIA Corporation GeForce GTX 1080/PCIe/SSE2
    Driver Version:  4.6.0 NVIDIA 455.45.01
    OpenGL Version: 4.6
    Desktop Color Depth: 24 bits per pixel
    Monitor Refresh Rate: 143 Hz
    VendorID:  0x10de
    DeviceID:  0x1b80
    Revision Not Detected
    Number of Monitors:  2
    Number of Logical Video Cards:  1
    Primary Display Resolution:  2560 x 1440
    Desktop Resolution: 4480 x 1440
    Primary Display Size: 27.44" x 15.43" (31.46" diag)
                                            69.7cm x 39.2cm (79.9cm diag)
    Primary Bus: PCI Express 16x
    Primary VRAM: 8192 MB
    Supported MSAA Modes:  2x 4x 8x 16x 

Sound card:
    Audio device: USB Mixer

Memory:
    RAM:  64256 Mb

VR Hardware:
    VR Headset: None detected

Miscellaneous:
    UI Language:  English
    LANG:  en_US.UTF-8
    Total Hard Disk Space Available:  400001 Mb
    Largest Free Hard Disk Block:  52390 Mb

Fixed with https://www.reddit.com/r/Fedora/comments/jxuh9i/cant_go_full_screen_mode_in_csgo/gczrzqq.

just ran into this trying to play TF2 with a friend, on Ubuntu 20.04 with the NVidia binary drivers. this is definitely not fixed in current releases.

note that using -windowed allows it to start in a window, choosing a fullscreen mode doesn't actually set things to fullscreen or switch out of windowed mode. so something is more broken now than it was initially in 2013.

I'm getting this on Ubuntu 20.10 too, with nVidia 455.xx drivers.

The game always starts in a 640x480 window unless I force the width/height parameters on it, and bricks whenever I make any changes via the settings prompt. The "fullscreen" option never works, but setting it from within the game settings window sometimes works and sometimes doesn't.

I'm getting this on Ubuntu 20.10 too, with nVidia 455.xx drivers as well