Since the JTAG pin does not have a clampode, it is pulled up with 2.5 V as a measure against exceeding the absolute maximum rating of 4.1 V.
Basically, there is no problem as long as the voltage does not exceed 4.1V.
Please refer to the following document.
Cyclone® 10 LP Core Fabric and General Purpose I/Os Handbook
https://docs.altera.com/r/docs/683777/current/cyclone-10-lp-core-fabric-and-general-purpose-i/os-handbook/logic-elements
(6.1.4.3. JTAG Single-Device Configuration section)
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Category: Configuration Programming
Tools:-
Device: Cyclone® 10 LP