If there are any heating commands in the custom start gcode Slic3r won't put them in by itself. So you can do something like
M109 S[first_layer_temperature_0] ; heat up nozzle
G12 ; clean nozzle
in your startup code so you can get the behavior you want. I use this on my printer so the bed heats up before I home (I use an inductive sensor in the middle of the bed so I want the bed to do any warping before probing). The relevant section of my start gcode looks like this:
M190 S[first_layer_bed_temperature]
G4 S30 ; Wait for bed temperature to stabilize
G28 ; home all axes
M420 L0 ; Load UBL matrix
M420 S1 ; Activate UBL
M420 Z10.0 ; 10mm fade height
G0 F6000 X40 Y-5 Z0.5 ; Somewhere ooze isn't a problem
M109 S[first_layer_temperature]
M150 R255 B255 U255 W255 ; Let there be light!
; Extrude a bit so we end up knocking it off with the edge of the bed
M83 ;Extruder relative
G0 F200 E7.5 ; Extrude a bit (should end up extruding about 15cm with a 0.4 nozzle)
G0 E-0-.5; retract