That's not the way to think on this issue.
1/3 of the Jinnah-class frigate program is about building the PN's expertise in designing a modern warship.
1/3 is about building Pakistan's ability to manufacture these ships by using the subsystems, inputs, etc, they want. So, even though we can't make 99% of this ship domestically, we can at least work with the suppliers we want (and not the OEM's partners). This helps us lower the cost and, potentially, start getting targeted ToT in specific areas like steel or other critical inputs at an industry level. E.g., if KSEW contracts "Sindhi Society Steel" to supply the steel by buying it from a South Korean partner, then "Sindhi Society Steel" might try to produce some of that steel in Pakistan so as to increase its profits (by using local manpower, currency, etc).
1/3 is on designing an affordable platform that the PN could acquire in larger numbers. In all likelihood, the decision for the 16 VLS likely came from the PN itself. Part of the reason for just 16 stems from the CAMM-ER SAM. This is an amazing SAM, but we don't have a quad-pack VLS solution (France probably denied selling us the SYLVER). So, we're stuck with the current VLS you see there. This is what happens when we constantly import instead of developing indigenous solutions. If we had thought about developing SAMs back in the 1990s, we might have had a quad-pack VLS solution today.
I get you're trying to think in terms of capability, but you got it wrong. In fact, you're assuming the Type 054A is superior to the Jinnah-class just because of it having 32 cells, but if you spent time reading this forum you'd know the J-Class has a lot more going for it. For starters, the J-Class' SAM system -- CAMM-ER -- is in another league compared to the Type 054A's old SARH HQ-16.