Purpose: We compare the effects of scatter on the accuracy of areal bone mineral density (BMD) measurements obtained using two flat-panel detector (FPD) dual-energy (DE) imaging configurations: a dual-kV acquisition and a dual-layer detector. Methods: Simulations of DE projection imaging were performed with realistic models of x-ray spectra, scatter, and detector response for dual-kV and dual-layer configurations. A digital body phantom with 4 cm Ca inserts in place of vertebrae (concentrations 50 - 400 mg/mL) was used. The dual-kV configuration involved an 80 kV low-energy (LE) and a 120 kV high-energy (HE) beam and a single-layer, 43x43 cm FPD with a 650 μm cesium iodide (CsI) scintillator. The dual-layer configuration involved a 120 kV beam and an FPD consisting of a 200 μm CsI layer (LE data), followed by a 1 mm Cu filter, and a 550 μm CsI layer (HE data). We investigated the effects of an anti-scatter grid (13:1 ratio) and scatter correction. For the correction, the sensitivity to scatter estimation error (varied ±10% of true scatter distribution) was evaluated. Areal BMD was estimated from projection-domain DE decomposition. Results: In the gridless dual-kV setup, the scatter-to-primary ratio (SPR) was similar for the LE and HE projections, whereas in the gridless dual layer setup, the SPR was ~26% higher in the LE channel (top CsI layer) than in the HE channel (bottom layer). Because of the resulting bias in LE measurements, the conventional projection-domain DE decomposition could not be directly applied to dual-layer data; this challenge persisted even in the presence of a grid. In contrast, DE decomposition of dual-kV data was possible both without and with the grid; the BMD error of the 400 mg/mL insert was -0.4 g/cm2 without the grid and +0.3 g/cm2 with the grid. The dual-layer FPD configuration required accurate scatter correction for DE decomposition: a -5% scatter estimation error resulted in -0.1 g/cm2 BMD error for the 50 mg/mL insert and a -0.5 g/cm2 BMD error for the 400 mg/mL with a grid, compared to <0.1 g/cm2 for all inserts in a dual-kV setup with the same scatter estimation error. Conclusion: This comparative study of quantitative performance of dual-layer and dual-kV FPD-based DE imaging indicates the need for accurate scatter correction in the dual-layer setup due to increased susceptibility to scatter errors in the LE channel.