Transmission spectra probe the atmospheres of transiting exoplanets, but these observations are also subject to signals introduced by magnetic active regions on host stars. Here we outline scientific opportunities in the next decade for providing useful constraints on stellar photospheres and inform interpretations of transmission spectra of the smallest ($R<4,R_{odot}$) exoplanets. We identify and discuss four primary opportunities: (1) refining stellar magnetic active region properties through exoplanet crossing events; (2) spectral decomposition of active exoplanet host stars; (3) joint retrievals of stellar photospheric and planetary atmospheric properties with studies of transmission spectra; and (4) continued visual transmission spectroscopy studies to complement longer-wavelength studies from $textit{JWST}$. We make five recommendations to the Astro2020 Decadal Survey Committee: (1) identify the transit light source (TLS) effect as a challenge to precise exoplanet transmission spectroscopy and an opportunity ripe for scientific advancement in the coming decade; (2) include characterization of host star photospheric heterogeneity as part of a comprehensive research strategy for studying transiting exoplanets; (3) support the construction of ground-based extremely large telescopes (ELTs); (4) support multi-disciplinary research teams that bring together the heliophysics, stellar physics, and exoplanet communities to further exploit transiting exoplanets as spatial probes of stellar photospheres; and (5) support visual transmission spectroscopy efforts as complements to longer-wavelength observational campaigns with $textit{JWST}$.
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