This ambiguity remains, they (assessing bodies) gave conflicting equivalence for the same degrees acquired from the same institutes. Like you have described an engineering degree should be equal to a 4 year one, as HEC's devised curriculum is comparable to international standards.If you want to claim points for two or more degrees/certificates then you can enroll in PGD from VU, and you will definitely be able to get your desired ECA if you already have a Bachelor's degree. Being an overseas student, I paid USD 1680 (~260,000 PKR) for my one-year PGD, just to claim those marks. For Pakistani students, the fee is much less and is definitely worth it.
I did not send my PGD to WES so I do not have an idea how they assess the diploma from VU, but IQAS gave me the ECA of two or more certificates. IQAS usually assess Pakistani degrees as per HEC, so if your degree is recognized by HEC as a 4 years bachelor's, IQAS assess it as 4 years bachelor's. You can see the IQAS credential template for the Pakistani degrees here.
Let me also share my experience with WES, last year I sent my wife's 4 years engineering degree from MUET and my 4-years bachelor's degree from Sindh university plus a level 5 Australian diploma from and an Australian Institute for assessment. They recognized my wife's 4-years degree as equivalent to Candian's 4-years Bachelors degree. However, for my bachelor's degree, they gave the equivalency of 3-year bachelors and recognized my diploma as "Completion of College-level certificate (One-semester)". Also, on the summary of the ECA report, they just mentioned my 3-year bachelor's degree and did not include a diploma in the summary of the ECA report because they did not consider it as completed.
Please note that IRCC will give you marks for two or more certificates only if the summary of your WES ECA (at the top of the report) says that you have 3/4 years bachelor's degree and 1-year or more PGD/postgraduate/college-level certificate. This is as per my correspondence with IRCC's help center, immigration officer may consider two separate reports from different bodies so contact them to get further clarification on it.
Disclaimer: This is my experience with different assessment bodies, yours could be different based on your circumstances. So please do your own research to see if you will be able to get the desired outcome.