I discovered two issues with the creation and use of .toml files:

a) I first created for my ESP32S3 display a custom board directory and created all the files in line with your MY_CUSTOM_BOARD example. That compiled and worked as expected. After that I created a .toml file in same directory, including all the pin configuration etc.
Compiling again with
python3 make.py esp32 --custom-board-path=../../esp32/ELECROW_DLC35010R DISPLAY=ili9488 INDEV=ft6x36
ends with an error:

Compiling....
Getting ESP-IDF build Environment
Traceback (most recent call last):
  File "/home/hermoers/projects/esp32/lvgl_micropython/make.py", line 330, in <module>
    mod.compile(*extra_args)
  File "/home/hermoers/projects/esp32/lvgl_micropython/builder/esp32.py", line 1452, in compile
    cmd_.extend(args)
TypeError: 'NoneType' object is not iterable

I think the problem is in esp32.py, function build_sdkconfig(*args), line 1304, called from compile(*args), line 1429. As there is no return value, all the arguments which were created from the toml file get lost.

b) I moved the .toml file into a separate directory and compile with
python3 make.py --toml=../../esp32/ELECROW_DLC35010R_TOML/elecrow_dlc35010r.toml
That does compile without an error, but the module touch (ft6x36) is not included.

my .toml file is as follows:

[MCU.esp32]
BOARD = "ESP32_GENERIC_S3"
BOARD_VARIANT = "SPIRAM_OCT"
flash_size = 16
enable_jtag_repl = 'n'
enable_cdc_repl = 'n'
enable_uart_repl = 'y'
uart_repl_bitrate = 115200

[I80Bus.display_bus]
data0 = 47
data1 = 21
data2 = 14
data3 = 13
data4 = 12
data5 = 11
data6 = 10
data7 = 9
data8 = 3
data9 = 8
data10 = 16
data11 = 15
data12 = 7
data13 = 6
data14 = 5
data15 = 4
dc = 45
wr = 18
cs = -1
freq = 40_000_000

[I2C.Bus.i2c_bus]
host = 0
scl = 39
sda = 38
freq = 100_000

[I2C.Device.indev_device]
bus = "i2c_bus"
dev_id = "ft6x36.I2C_ADDR"
reg_bits = "ft6x36.BITS"

[FT6x36.indev]
device = "indev_device"

[ILI9488.display]
data_bus = "display_bus"
display_width = 320
display_height = 480
backlight_pin = 46
color_byte_order = "ili9488.BYTE_ORDER_BGR"
color_space = "lv.COLOR_FORMAT.RGB565"

[ILI9488.display.init]
params = []

[display.set_color_inversion]
params = [false]

[display.set_rotation]
params = ["lv.DISPLAY_ROTATION._0"]

[display.set_backlight]
params = [100]

[task_handler.TaskHandler]
params=[]

I think the problem is in toml_reader.py lines 268/269. "ft6x36.I2C_ADDR" in my .toml fle is parsed there, the import statement ist written, 'ft6x36' is appened to the list used_imports. But it is not appended to the list self.imports, which ist scanned in line 500! If I change dev_id and reg_bits to numeric values, the module is included as expected.
In lines 222/223 and 243/244 potentially the same problem would show up.

Thanks for your fantastic job. The TOML file makes life much easier. Maybe you can mention in the README, that importing the display module ist the trick to get access to the TOML entries, It took me quite a while to figure that out ;)

Herbert