By default prefix is set to /usr/local

wpa_supplicant-2.0/wpa_supplicant/Makefile

export LIBDIR ?= /usr/local/lib/
export BINDIR ?= /usr/local/sbin/

but should be /usr/lib and /usr/sbin, can be corrected by specifying environment variables

define WPA_SUPPLICANT_BUILD_CMDS
        $(TARGET_MAKE_ENV) CFLAGS="$(WPA_SUPPLICANT_CFLAGS)" \
                LDFLAGS="$(TARGET_LDFLAGS)" LIBDIR=/usr/lib/ BINDIR=/usr/sbin/ \
                $(MAKE) CC="$(TARGET_CC)" -C $(@D)/$(WPA_SUPPLICANT_SUBDIR)
endef

These variables are used for generating service files for В-Bus and Systemd

[D-BUS Service]
Name=fi.w1.wpa_supplicant1
Exec=@BINDIR@/wpa_supplicant -u
User=root
SystemdService=wpa_supplicant.service