TL;DR: My current position does not afford me the opportunity to gain experience in some tasks that are viewed as standard junior level tasks for my industry. How does this affect my chances of getting a job with the same title/responsibilities at a different company?
Introduction
For the past 2.5 years, I have worked as a contractor as a junior/early career geologist at a small company that provides onsite technical support/assistance to a United States federal agency. I have done fairly well in my capacity as a geologist and the government PM (who I essentially report to) at this federal agency holds me in high regard with respect to my abilities, competency, and work ethic (said PM is vocal of their satisfaction and has encouraged me to apply to vacant federal positions within the agency).
With all this being said, my job responsibilities as an early career geologist in some respects are quite different when compared to say someone who is a junior geologist with the same years of experience as me but at a different company. A general example of this might be: A geologist is expected to log cuttings/cores produced from drilling wells. This is generally considered to be the real first step in working toward a senior geologist position in industry, while I as a geologist with the same years of experience am expected to observe/oversee the execution of this logging/fieldwork while never having performed this task professionally myself. As my education has given me the training and skill-sets to understand the "ins and outs" of drilling and logging and how it should be performed/executed, to me it doesn't seem inappropriate for me to observe/oversee this task. That being said, I have never performed drilled/logged professionally nor will I ever been give the opportunity in my current position.
It should be noted that my time in this position has also given me a lot of responsibilities that only mid to senior level geologist/scientists are tasked with. The flip-side to this is that in being given nontraditional roles and responsibility as a junior staff, I have not been given some of the more traditional junior geologist duties that most people with my time and experience are given.
Problem
It is likely that my contract will not be renewed in the coming year and as such I am looking to secure new employment as a early career geologist but at a different company. I am looking to stay in the same industry as well.
I have applied to multiple junior/early career geologist openings that are commensurate with my experience,education, and training at various other companies but as of yet, I have not secure new employment. I have interviewed a few times but no offers.
Question
What is the likelihood that my nontraditional career beginnings will have a negative affect on my chances of getting a job as a early career geologist at a different company in the same industry?
Further Clarification:
1: I work in the environmental remediation industry.
Edit
Added more details relating to my job position, title, and country.