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Configuration tools like eduroam CAT enable to provision the chosen CA(s) and the expected server name(s) into client devices without user interaction. In that light, it does not make much difference whether to procure a server certificate from a commercial CA or to make your own; either way, configuration steps are necessary to enable your chosen setup. With the conceptual differences being small, a number of secondary factors come into play when making the decision where to get a server certificate from:
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