Sure, the project template is C:\Program Files\KiCad\share\kicad\template\kicad.pro. You will need admin rights to change it. so for example run notepad as admin (right click over notepad icon and choose “Run as administrator”)
Then you need to change the following lines.
[eeschema/libraries]
LibName1=power
LibName2=device
LibName3=transistors
LibName4=conn
LibName5=linear
LibName6=regul
LibName7=74xx
LibName8=cmos4000
LibName9=adc-dac
LibName10=memory
LibName11=xilinx
LibName12=microcontrollers
LibName13=dsp
LibName14=microchip
LibName15=analog_switches
LibName16=motorola
LibName17=texas
LibName18=intel
LibName19=audio
LibName20=interface
LibName21=digital-audio
LibName22=philips
LibName23=display
LibName24=cypress
LibName25=siliconi
LibName26=opto
LibName27=atmel
LibName28=contrib
LibName29=valves
to
[eeschema/libraries]
LibName1=74xgxx
LibName2=74xx
LibName3=ac-dc
LibName4=actel
LibName5=adc-dac
LibName6=allegro
LibName7=Altera
LibName8=analog_devices
LibName9=analog_switches
LibName10=atmel
LibName11=audio
LibName12=battery_management
LibName13=bbd
LibName14=bosch
LibName15=brooktre
LibName16=cmos4000
LibName17=cmos_ieee
LibName18=conn
LibName19=contrib
LibName20=cypress
LibName21=dc-dc
LibName22=device
LibName23=digital-audio
LibName24=diode
LibName25=display
LibName26=dsp
LibName27=elec-unifil
LibName28=ESD_Protection
LibName29=ftdi
LibName30=gennum
LibName31=graphic
LibName32=hc11
LibName33=intel
LibName34=interface
LibName35=ir
LibName36=Lattice
LibName37=leds
LibName38=linear
LibName39=logo
LibName40=maxim
LibName41=mechanical
LibName42=memory
LibName43=microchip
LibName44=microchip_dspic33dsc
LibName45=microchip_pic10mcu
LibName46=microchip_pic12mcu
LibName47=microchip_pic16mcu
LibName48=microchip_pic18mcu
LibName49=microchip_pic24mcu
LibName50=microchip_pic32mcu
LibName51=microcontrollers
LibName52=modules
LibName53=motorola
LibName54=motors
LibName55=motor_drivers
LibName56=msp430
LibName57=nordicsemi
LibName58=nxp
LibName59=nxp_armmcu
LibName60=onsemi
LibName61=opto
LibName62=Oscillators
LibName63=philips
LibName64=power
LibName65=powerint
LibName66=Power_Management
LibName67=pspice
LibName68=references
LibName69=regul
LibName70=relays
LibName71=rfcom
LibName72=sensors
LibName73=silabs
LibName74=siliconi
LibName75=stm32
LibName76=stm8
LibName77=supertex
LibName78=switches
LibName79=texas
LibName80=transf
LibName81=transistors
LibName82=triac_thyristor
LibName83=ttl_ieee
LibName84=valves
LibName85=video
LibName86=wiznet
LibName87=Worldsemi
LibName88=Xicor
LibName89=xilinx
LibName90=zetex
LibName91=Zilog
which works for 4.0.6, there might be some differences to 4.0.5.