Chapters 3 and 4 concentrated upon the affinities that underpinned Rational Dissenting theology and the nuances, and sometimes tensions, within these affinities. Chapters 5 and 6 move on to analyse the ways in which the significant differences that separated Rational Dissenting from orthodox theology led to differences in ideas and argument on issues of liberty. The argument of these two chapters is that the Rational Dissenting concepts of liberty were the direct outcome of their specific theological identity.

The theological basis of Rational Dissenting ideas on liberty has so far received relatively little scholarly attention. Robert Hole's important study of 1989 touched upon religious arguments relating to liberty and politics, but his book's first priority was the application of religious ideas to support the traditional order in Church and state. The main emphasis of H. T. Dickinson's Liberty and Property viewed its subject in essentially secular terms. Although many (but far from all) Dissenters participated in campaigns for reform, as many historians have noted, the theological motivation behind their political involvement remains relatively unexplored. J. C. D. Clark's challenge to this approach is apposite:

With the proviso that ‘suspicion and conflict’ between Dissenters concerned doctrine as well as ecclesiastical polity, Professor Clark reminds us of the need for a detailed exploration of Rational Dissenting concepts of liberty, looking not just at the views of a handful of key players but what we can glean from the ‘hinterland’ – the lesser-known individuals, chapels, societies, publications, and private documents. Rational Dissenters other than Price and Priestley have not so far received sufficient close attention. Although Martin Fitzpatrick has devoted attention to other Rational Dissenters, Priestley's commitment to universal toleration has been his principal subject of enquiry. James E. Bradley's assertion that ‘provincial Dissenting ministers are especially important because they linked local to national political issues’ is highly relevant to the present discussion, but his most detailed analysis is based on detailed analysis of three Orthodox and only two Rational Dissenting ministers.