pursuing PhD without relevant bachelor degree
From the research I found all I can say
This a list of United States universities with GIS PhD programs

You have a MSc in GIS even with pass, just go ahead and submit your undergraduate transcript. The admissions committee will be expecting to see one (BSc Or MSc) and your application might be screened out before consideration simply because this transcript is missing.

The fact that you've had GIS master may help to overcome the bad impression left by your BSc (even in my way of thinking there is no bad impression). 
Having a good letters of recommendation and one or more publications (of high quality) will help a lot more.

You certainly need to address this matter in your application, mostly by highlighting your recent MSc in GIS and explaining what has changed in your life so that you are going to be the good student.