I talked to Rabbi Welcher about the difficulty of paskening for BTs.
In a nutshell, at the beginning, the basic psak strategy for a BT just starting out is to be lenient. But as the BT grows in their knowledge and observance, they move towards the normative halacha, and then as they continue to grow, they might well be machmir in situations that a yeshiva student, Kollel member or Rabbi/Rebbi would be machmir.
But the issue is dependent on the exact halachic area. If there is no difficulty in the BT following the normative halacha, it might be appropriate to follow normative halacha, and not be lenient, even in the beginning.
A second difficulty is how to assess exactly when and if the BT crosses various thresholds and grows in their Torah observance.
A third difficulty is that because of non religious family situations, BTs have a lot of complex shailos with many factors to consider.
Rabbi Welcher related that he once said to Rabbi Moshe Halberstam z”tl (niftar in 2006) that his only complaint as a posek was that he would like to trade the difficult questions that Rav Chaim Ozer Grodzinski z”tl (niftar in 1940 and one of the major poskim of the last 100 years) answered with the Baalei Teshuva shailos that have to be dealt with today. (The number of Baalei Teshuva grew massively after 1967). Rabbi Halberstam smiled knowingly.
So Baalei Teshuva can take solace in the fact that our shailos are among the most difficult. The flipside is that BT Rebbeim really need to know their halachic stuff.