Pull-up GPIO high in u-boot

I need the TK1 pins 200 and 204 pulled-high after poweron. I compiled u-boot with following in board/toradex/apalis-tk1/pinmux-config-apalis-tk1.h

static const struct tegra_gpio_config apalis_tk1_gpio_inits[] = {
	/*        port, pin, init_val */
	...
	GPIO_INIT(A,    2,   IN),
	GPIO_INIT(A,    3,   IN),
        ...
};

...

static const struct pmux_pingrp_config apalis_tk1_pingrps[] = {
	/*     pingrp,                 mux,          pull,   tri,      e_input, od,      rcv_sel */
	...
	PINCFG(DAP2_FS_PA2,            HDA,          UP,     NORMAL,   INPUT,   DEFAULT, DEFAULT),
	PINCFG(DAP2_SCLK_PA3,          HDA,          UP,     NORMAL,   INPUT,   DEFAULT, DEFAULT),
        ...
};

static const struct pmux_drvgrp_config apalis_tk1_drvgrps[] = {
};

When I check the pin levels in u-boot they seem to be not pulled up:

Apalis TK1 # gpio input A2
gpio: pin A2 (gpio 2) value is 0
Apalis TK1 # gpio input A3
gpio: pin A3 (gpio 3) value is 0

Those pins don’t support pulls in any direction. They’re connected to level shifter before they reach TK1 Soc. Level shifter direction is being controlled by GPIO S3, if S3 is low direction is GPIO A3 ← TK1 pin 200, and when high GPIO A3 → TK1 pin 200 (same goes for A2 and 204).
According to the Apalis standards those pins are fixed function digital audio signals. When using them for different function you have no guarantee of support in future versions of both software and hardware, as well as on different modules in Apalis family.