Each aircraft, regardless if it is a new/refined variant or of the same caliber, goes through customer acceptance flights (CAF). The customer - i.e., IAF - needs to be satisfied with each aircraft before induction.
Also, manufacturers almost always retain one or more - usually the first aircraft - as dedicated prototype or testbed to continue testing, making improvements, and systems validation even after CAF. This is done for every new variant/block. Assume, an error/fault is found later [post-production/post-induction] in the prototypes/testbeds the manufacturer can resolve the issue proactively and introduce problem solving to the inducted aircraft in timely manner rather than to have the customer find out the problem, ground the entire fleet, and ask the manufacturer to reactively solve the issue.
Hence, it doesn't matter if MK1 and MK1A a structurally the same. There needs to be a prototype of MK1A. If you look at videos of PAC or CAC you will usually find prototypes of JF-17 (including Blk 3) and J-10 (CAC only) at their plants. Lockheed, Boeing, etc., all retain a few aircraft of the new variants for continious testing, improvements, and advancements.