If you get ur immobilizer proffesional installed(which you should, no point risking your car for a few bucks) with the turbo timer, it will have no ill effects whats so ever.
Im running a good alarm (Wont mention brand) and turbo timer, both were installed at the same time.
I can have my turbo timer on for 2 or 3 mins, arm my alarm, and the alarm will activate. If someones breaks into ur car while the turbo timer is on, and tries to drive the car away, the alarm will turn off the turbo timer immediately.
So no, it wont have any effects on ur immobiliser.
However i do recommend you go for a full alarm system rather then just the immobiliser... too many skylines get stolen now a days.
Hope this helps
Brendan