Does the head follow the heart in matters of truth?

[Angrboda]

I suppose a related question is, given we follow the same psychological limits in acquiring and shoring up our beliefs as theists, are we in any sense justified in believing that our positions are rationally better justified than theirs?

In general, yes, I think so. Just because we share the same psychological limits doesn't mean we deal with those limits in the same way. However, short of psychological studies to assess the differences between atheists and theists when it comes to this subject, I can't be too sure. Personally, I value the use of logic, reasoning, and empirical evidence, regardless of the comfort factor of whatever truth they may lead me to. This is not to say I can't ever be biased, but that when I am made aware of any such biases that may be misguiding me, I like to think that I make an effort to acknowledge them and do my best to keep them "at bay". And correct any misconceptions I may have had due to such biases.

The bias blind spot is the cognitive bias of recognizing the impact of biases on the judgment of others, while failing to see the impact of biases on one's own judgment. The term was created by Emily Pronin, a social psychologist from Princeton University's Department of Psychology, with colleagues Daniel Lin and Lee Ross. The bias blind spot is named after the visual blind spot. Most people appear to exhibit the bias blind spot. In a sample of more than 600 residents of the United States, more than 85% believed they were less biased than the average American. Only one participant believed that he or she was more biased than the average American. People do vary with regard to the extent to which they exhibit the bias blind spot. It appears to be a stable individual difference that is measurable (for a scale, see Scopelliti et al. 2015).

The bias blind spot appears to be a true blind spot in that it is unrelated to actual decision making ability. Performance on indices of decision making competence are not related to individual differences in bias blind spot. In other words, everyone seems to think they are less biased than other people, regardless of their actual decision making ability.

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Bias blind spots may be caused by a variety of other biases and self-deceptions....People also tend to believe they are aware of "how" and "why" they make their decisions, and therefore conclude that bias did not play a role. Many of our decisions are formed from biases and cognitive shortcuts, which are unconscious processes. By definition, people are unaware of unconscious processes, and therefore cannot see their influence in the decision making process.

Wikipedia || Bias blind spot

The introspection illusion is also relevant, but I will only quote in part. The full article deserves a read.

The introspection illusion is a cognitive bias in which people wrongly think they have direct insight into the origins of their mental states, while treating others' introspections as unreliable. In certain situations, this illusion leads people to make confident but false explanations of their own behavior (called "causal theories") or inaccurate predictions of their future mental states.

The illusion has been examined in psychological experiments, and suggested as a basis for biases in how people compare themselves to others. These experiments have been interpreted as suggesting that, rather than offering direct access to the processes underlying mental states, introspection is a process of construction and inference, much as people indirectly infer others' mental states from their behavior.

When people mistake unreliable introspection for genuine self-knowledge, the result can be an illusion of superiority over other people, for example when each person thinks they are less biased and less conformist than the rest of the group. Even when experimental subjects are provided with reports of other subjects' introspections, in as detailed a form as possible, they still rate those other introspections as unreliable while treating their own as reliable. Although the hypothesis of an introspection illusion informs some psychological research, the existing evidence is arguably inadequate to decide how reliable introspection is in normal circumstances. Correction for the bias may be possible through education about the bias and its unconscious nature.

Wikipedia || Introspection illusion