Physical unclonable functions (PUFs) are a handy security primitive for resource-constrained devices. They offer an alternative to the resource-intensive classical hash algorithms. Using the IC differences resulting from the fabrication process, PUFs give device-specific outputs (responses) when given the same inputs (challenges). Hence, without using a device-specific key, PUFs can generate device-specific responses. FPGAs are one of the platforms that are heavily studied as a candidate for PUF implementation. The idea is that a PUF that is designed as an HDL code can be used as part of the static design or as a dynamic accelerator. Previous works studied PUF implementation as part of the static design. In contrast to the state-of-the-art, this letter studies PUFs when used as runtime reconfigurable accelerators. In this letter, we find that not all regions of an FPGA are equally suitable for implementing different PUF types. Regions, where clock routing resources exist, are the worst suited for PUF implementation. Moreover, we find out that for certain PUF types, the property of dynamic partial reconfiguration can lead to performance degradation if not applied carefully. When static routing passing through the region increases, the PUF performance degrades significantly.