Developing and evolving today's systems are often stymied by the sheer size and complexity of the capabilities being developed and integrated. At one end of the spectrum, we have sophisticated agent-based software with hundreds of thousands of collaborating nodes. These require modeling abstractions relevant to their complex workflow tasks as well as predictable transforms and mappings for the requisite elaborations and refinements that must be accomplished in composing these systems. At the other end of the spectrum, we have ever-increasing capabilities of reconfigurable hardware devices such as field-programmable gate arrays to support the emerging adaptability and flexibility needs of these systems. From a model-based engineering perspective, these challenges are very similar; both must move their abstraction and reuse levels up to meet growing productivity and quality objectives. Model-based engineering and software system variants such as the model-driven architecture (MDA) are increasingly being applied to systems development as the engineering community recognizes the benefits of managing complexity, separating key concerns, and automating transformations from high-level abstract requirements down through the implementation. However, there are challenges when it comes to establishing the correct boundaries for change-tolerant parts of the system. Capabilities engineering (CE) is a promising approach for defining long-lived components of a system to ensure some sense of change tolerance. For innovative initiatives such as the National Aeronautics and Space Administration (NASA)'s autonomous nanotechology swarms (ANTS), the development and subsequent evolution of such systems are of considerable importance as their missions involve complex, collaborative behaviors across distributed, reconfigurable satellites. In this paper, we investigate the intersection of these two technologies as they support the development of complex, change-tolerant systems. We present an effective approach for bounding computationally independent models so that, as they transition to the architecture, capabilitiesbased groupings of components are relevant to the changetolerant properties that must convey in the design solution space. The model-based engineering approach is validated via a fully functional prototype and verified by generating nontrivial multiagent systems and reusing components in subsequent systems. We build off of this research completed on the collaborative agent architecture, discuss the CE approach for the transition to architecture, and then examine how this will be applied in the reconfigurable computing community with the new National Science Foundation Center for High-Performance Reconfigurable Computing. Based on this work and extrapolating from similar efforts, the modelbased approach shows promise to reduce the complexities of software evolution and increase productivity-particularly as the model libraries are populated with canonical components.