In older versions of pdf-presenter-console it was not possible for i3 to differentiate between the presenter and presentation container. With the new version available in strech (3.1.1+git.1.5d18a2c-1) there is the window role set for each window. Now it is very easy to put the screens right to the correct one:

for_window [window_role="presentation" class="(?i)pdf-presenter-console"] move container to output right
for_window [window_role="presenter" class="(?i)pdf-presenter-console"] move container to output LVDS1

In my case the presenter console will always be on the internal laptop monitor. The presentation screen goes directly to the next attached monitor (considering there is only one extra monitor...). I do not exactly know why, but you have to do the second line as well, because otherwise both containers are moved to the second monitor. I think the problem occurs because the presenter window spawns after the presentation window and the focus is now on the second monitor. Maybe you can prevent this by moving the presentation container to a special workspace, which is always on the second monitor.

Something like

for_window [window_role="presentation" class="(?i)pdf-presenter-console"] move container to workspace presentation, move workspace presentation to output right
for_window [window_role="presenter" class="(?i)pdf-presenter-console"] move container to workspace presenter, move workspace presenter to output LVDS1, focus workspace presenter

But i did not tested that...