When you have two packs in series, the current flowing through each pack is identical, it has to be because there is no other path for current to flow. The pack doesn't know if it is being used in a series configuration or by itself. All it 'sees' is current flowing and it's your job to have the current stop flowing before the battery is 'flat'. Your batteries are rated in mAh, literally current hours. The higher the current flowing through the battery, the sooner it will be 'flat'! Twice the current, half the run time. Ten times the current, 1/10th the run time. If you have a 5000mAh battery then you expect that you can draw 5000mA = 5A constant for 1 hour before it is 'flat' i.e. 100% discharged i.e. 3.0V/cell. If you draw 50A constant then it will be 'flat' in 1/10th of an hour - 6 minutes.

If two packs are in series and one pack is 4500mAh while the other is 5000mAh then at the same 50A draw the 4500mAh pack will be 'flat' in 5 minutes and 24 seconds, hitting 3.0V/cell while the 5000mAh pack which has been discharging at exactly the same rate still has 500mAh left (5000 minus 4500) i.e. it is 90% discharged so you'd expect it to be around 3.6V/cell. Now, it's your job to work out what the cutoff voltage should be when you use those two packs together so that the 4500mAh pack doesn't get below 3.0V/cell before the LVC cuts in. So for safety, you might have the LVC set so that it cuts in when there is 250mAh (95% discharge = ~3.4V/cell) left in the 4500mAh pack and therefore 750mAh (85% discharge = ~3.7V/cell) left in the 5000mAh pack. That way you still have a good 0.4V/cell safety margin. If they are both 2S packs, then your LVC becomes 3.4*2+3.7*2 = 14.2V, simples!

As far as internal resistance goes, it does not reduce the actual capacity of the battery however it becomes a hindrance in terms of turning stored chemical energy into electricity. Consider a 2S battery that has 5mOhm cell internal resistance. For two cells, we have 10mOhm total. If we draw 50A then we cause a voltage drop of 50A*0.010ohm = 0.5V. So when drawing 50A constant then 0.5V/7.4V = 6.7% of the packs capacity is lost as heat. So your 5000mAh pack only puts out 4665mAh of electrical energy and the rest as heat. If you drew a very low current almost all 5000mAh would be able to be extracted as electrical energy. If another pack has half the resistance it only loses 3.4% as heat or if it were double it loses 13% as heat. That just factors into the previous example of a capacity mismatch. Unless your packs have a wildly different internal resistance AND you're drawing stupid currents almost constantly, it will therefore be a non issue as both packs should still have close enough capacity that a practical LVC voltage can be found that uses most of the capacity of both packs while halting things before any cell voltage becomes damagingly low.

If you buy two packs at the same time, same manufacturer and model, then both the capacity and internal resistance should be quite well matched.

If that all sounds too complicated, I have good news, you don't need to understand any of it to set up your LVC. As previously said, you just charge both batteries fully and run the car, stopping every minute or two and checking all cell voltages. When any cell gets close to 3.0V (use 3.4V instead for safety, you're only giving away 5% of your capacity), measure the total voltage and that is what your LVC should be set to. Every time you run the packs down to LVC, just check what all the cell voltages got to. If you notice one or more creeping down below 3.4V then up your LVC by 0.1V or 0.2V, then check how things are going again after the next run to see if it fixed the issue.
NEVER connect two packs in series which aren't both fully charged - that's asking for trouble. If you follow these rules and a pack degrades at an alarming rate when used in series then either the pack was defective and would have died quickly even if used by itself, or you failed at keeping all the cell voltages above 3.0V at all times.

Oh, and if you want to have more than one pair of batteries in rotation, you're going to have to set a much more conservative (higher) LVC unless you keep track of all your packs and set a specific LVC before each run!

Consider the following article:

U-803a: Cell Matching and Balancing

My take on this article is that it only discusses matched cells in a single pack, they explain how the cells are carefully grouped together when they are matched. It would be a bad assumption that 2 packs from the same manufacturer are matched, in fact you would have to be extremely lucky to get 2 matched packs at random... perhaps it might be possible to get 2 matched packs, but that would require you to use the same method that the manufacturer used to match the cells in the first place... this would not be practical which would require you to keep buying additional packs until you eventually find a matched set.

Another article here worth a read:

BU-806: Tracking Battery Capacity and Resistance as part of Aging

So the relationship between IR and capacity is through age in how they are directly related.

If you read my technical explanation above, you would realise that 10% or perhaps even up to 20% mismatch in capacity doesn't have to be a problem, just means that you adjust your LVC accordingly.

I would be very surprised if I bought a pack advertised as 5000mAh and it was in fact 4000mAh (-20%) or 6000mAh (+20%). All the batteries I have are no more than about 200mAh (<5%) off from what they were advertised as, and they aren't ultra expensive packs. Between cells in the same pack I am seeing anything between 0 and 5% mismatch.