Plant factories with artificial lighting (PFALs), with well-insulated and airtight structures, enable the production of large quantities of high-quality plants year-round while achieving high resource use efficiency. However, despite the controlled environment in PFALs, variations in plant individuals have been found, which affect productivity in PFAL operations. Plant phenotyping plays a crucial role in understanding how the surrounding microenvironment affects variations in plant phenotypes. In the current study, a modular phenotyping system for seedling production was developed, focusing on practicality and scalability in commercial PFALs. Experiments on seedlings, which strongly affect productivity, were conducted to obtain cotyledon unfolding time and the time series projected area of cotyledons and true leaves of individual seedlings of romaine lettuce (Lactuca sativa L. var. longifolia), using RGB images. This was also undertaken to analyze how the surrounding microenvironment of photosynthetic photon flux densities and nutrients affect growth variations for plant cohort research. In agreement with the actual measurements, variations in seedling growth were identified even under similar microenvironments. Furthermore, the results demonstrated larger variations in seedlings with higher relative growth. Aiming for simplified interactions of phenotypes with the microenvironment, management, and genotype, seedling selection and breeding with plant production in PFALs may enable plant uniformity and higher productivity.