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Magnetic solitons such as skyrmions and bimerons show great promise for both fundamental research and spintronic applications. Stabilizing and controlling topological spin textures in atomically thin van der Waals (vdW) materials has gained tremendous attention due to high tunability, enhanced functionality, and miniaturization. Here, we present an efficient spin-spiral approach based on first-principles, a method for mapping magnetic interactions from collective models onto arbitrary lattice symmetries, such as hexagonal and honeycomb lattices. Using atomistic spin models parametrized from first-principles, we predict the emergence of multiple topological spin textures in an all-magnetic vdW heterostructure Fe$_3$GeTe$_2$/Cr$_2$Ge$_2$Te$_6$ (FGT/CGT) -- an experimentally feasible system. Interestingly, the FGT layer favors out-of-plane magnetization, whereas the CGT layer prefers in-plane magnetocrystalline anisotropy. Néel-type nanoscale skyrmions are formed at zero field in the FGT layer due to interfacial Dzyaloshinskii-Moriya interaction (DMI), while nanoscale bimerons and antibimerons can co-exist in the CGT layer by the interplay between exchange frustration and DMI. Using the collective approach we apply, we reveal significant discretization effects in hexagonal and honeycomb geometries. In particular, we demonstrate that the lifting of geometric exchange frustration on the honeycomb significantly affects soliton barriers and pinning energetics. These fundamental results not only highlight the importance of spin simulations in discrete models for topological magnetism, especially in 2D materials, but may also help to pave the way for solitonic devices based on atomically thin vdW heterostructures.