We present a thorough and detailed investigation of baryon isocurvature models including realistic thermal histories, \ie, late or partial reionization of the universe and compact object formation after standard recombination. Constraints on these models are imposed from spectral distortion in the cosmic microwave background (CMB), number fluctuations in galaxy counts , and recent CMB anisotropy observations. Since the status of degree scale anisotropies is as yet unclear, the lack of spectral distortions is the most serious constraint on the spectral index of initial fluctuations: $-1.2 \simlt n \simlt -0.5-1.2 \simlt n \simlt -0.9$ in compact object dominated universes in order to avoid significant bias in galaxy formation. Full ionization of the universe before is also forbidden by this constraint. Intermediate scale CMB fluctuations which are significantly larger than standard CDM is a {\it robust} prediction of these models. Many models are consequently in conflict with the recent degree scale detections by Python, ARGO, and MSAM, \eg, compact object dominated models with $\Omega_0 \simlt 0.2$. Moreover, {\it all} models will be ruled out if the low CMB fluctuations on degree scales as detected by the SP91 13 point scan are confirmed. On the other hand, most models fare well compared with the high Tenerife and MAX detections.

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