The marginal difference in the underlying costs between the DS1054z and the MSO1104z aren't very relevant in understanding pricing. I'd suggest thinking about supply/demand and artificial scarcity aren't very useful either.
Rigol designed a product line of instruments built on a common platform. This is a practice pursued across a wide range of industries for at least half-a-century. Its so prevalent and entrenched because it makes economic sense, because it allows companies to spread their fixed cost for design and tooling over a large volume, and improves their bargaining position for sourcing the common components used across the product line. Within those constraints, pricing is set to serve the companies goals, generally a trade-off between short term profit and market share. Pricing to end users is also influenced by the agendas of distributors and retailers.
If, however, we accept simplistic free-market models for the actions of companies who function internally like planned command economies, the apparent scarcity of the 1054z in the months after its introduction need not be artificial. Rigol's production was/is almost certainly constrained by volume and cost considerations. Say production capacity and supplier terms limit them to making 1000 scopes a day. If they can sell 1000 MSO1104z scopes a day and 2000 DS1054z scopes a day, how do you think they are going to allocate their production assuming relatively small cost differences between the models? For profits the choice would seem obvious. For market share, it might seem like a wash, but I suspect that customers for the DS1054z are somewhat more willing to accept delays in getting their orders filled than that of the higher-margin product, and may still be in the market if supply constraints are eased.
Clearly though, Rigol has done a number of things right, otherwise we wouldn't be talking about them. I'm guessing that the DS1054z is at least profitable on its own and goes a long way to helping amortize the up-front costs of the entire product line.