My opinion is that you should determine the Physical Limit for the action the same way you determine the appopriate Attribute for determining the die pool. You take the Strength based on the action (Single Limb, average of several, or lowest of all involved) and use that to determine the Physical Limit. This doesn't violate the RAW since the book just says "When a particular limb is used for a test (such as leading an attack with your cyberarm), use the attribute for that limb (natural or cyber); in any other case, take the average value of all limbs involved in the task." It doesn't say use the attribute for that limb when determining the die pool.
I've never been very adamant about this method, because people always seem concerned about this causing "extra math" to be involved. But if you're making a character with cyberlimbs that have different attributes from your body, you already have some extra figuring out to do, and it isn't that hard to write out the different possibilities for your Physical Limit based on this assumption. Unless you're going completely wacky with all four limbs having different strengths, it should be pretty straightforward. Your group just needs to agree on how many "limbs" there are in a test that involves the whole body.
Personally, I go with 5 (2 arms, 2 legs, and torso). And to be clear since the Cybertorso is a shell, I've always ruled that it doesn't have its own attributes, you always use your meat body when determining tests involving your torso.
Say I have a weakling elf decker (Bod 1, Agi 2, Rea 2, Str 1, Physical Limit 2) that decides to get an awesome arm for doing sharpshooting (Str 5, Agi 7). For using the pistol one handed, he would use just the Agility and Strength of the arm to determine effects. Which would be Agility 7 and a Strength of 5 for determining Recoil (only one extra point of recoil, so no big deal really). When using just that arm to punch he would still use that Agility 7, but because of the boost to stats his Physical Limit is also upped to 4. If he were to try and pick up a rifle or other two-handed weapon, we use his averaged stats between the two arms (Str 3, Agi 5[9/2, rounded up]). That extra recoil is gone, because his other arm is so weak, and if we needed a Physical Limit it would be 3. For something full body but not carefully coordinated, he has a Str 2, Agi 3, Phys Limit 3. And carefully coordinated would of course use his fully natural stats (since they're all lower than the arm).
And I just record it on my sheet as that series of numbers: Natural (Augmented / Avg 2 limbs / Avg whole body)
Bod: 1
Agi: 2 (7 / 5 / 3)
Rea: 2
Str: 1 (5 / 3 / 2)
Phys: 2 (4 / 3 / 3)