The signal-to-noise ratio in Positron Emission Tomography (PET) improves with precise timing resolution. PET systems enabling the capability of Time-of-Flight (ToF) are nowadays available. This study assesses various data configurations, comparing the obtained timing performances applicable to ToF-PET systems. Different readout configurations were evaluated together with Silicon Photomultipliers (SiPMs) photosensors from the Fondazione Bruno Kessler (FBK), with and without the so-called metal trench (MT) technology. The tests were carried out with scintillation crystals of 3×3×5 mm3 (LYSO:Ce,Ca) from SIPAT. Two onboard FPGA-based systems, namely the Felix Time-to-Digital Converter (TDC) from Tediel S.r.l. and the ASIC-based FastIC from the University of Barcelona, along with custom-made high-frequency electronics (CM-HF), were compared. Considering only photopeak events, the best coincidence timing resolution (CTR) results obtained were 71 ps with the MT SiPMs. This result worsened to 88 ps with the old version of the same device that does not include the MT technology (called HD). The results demonstrate substantial CTR improvements when MT SiPMs were used across the different scenarios, resulting in a timing improvement in the 10 to 45 ps range compared to HD SiPMs. Notably, the Felix TDC achieved sub-100 ps timing results, emphasizing the potential of FPGA technology in ToFPET applications. Moreover, the fully passive version of the CMHF connected to the MT SiPMs shows only a degradation of 8 ps difference compared to the version using amplifiers. The novel MT-type SiPMs promise superior timing performance, enhancing accuracy and efficiency in PET imaging systems.