Not necessarily. It all depends exactly which four groups qualify a 3rd place team.
Assuming we win the group then we play one of A3/C3/D3. If ALL of those groups have their 3rd placed team qualify, then in the table I posted above there are 3 combinations for ACD all qualifying - ABCD, ACDE, ACDF. All of those result in playing group D's team which is likely going to be Czech Republic because of Turkey's rubbish goal difference.
If Northern Ireland finish 3rd in group C, there's only one combination of groups that will see us playing them - BCEF
There are 7 combinations each for playing the team from group A or group D, and just the one for group C. So it's virtually 50/50 going to be Albania or Czech Republic.
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As an aside, looking at group D, if Czech Republic beat Turkey by 2 goals and Croatia lose to Spain, then Croatia would drop to 3rd, because the Czech v Croatia game was 2-2 so head to head record would be equal and it'd go down to overall goal difference in the group. Then as mentioned above, we'd have almost a 50/50 chance of getting them instead of Albania.
Crazily though, if Croatia lose 1-0 and Czech Republic win 1-0 then everything would be exactly level between them and there'd have to be a penalty shootout between the two to decide who finished 2nd and 3rd!