There is no incompatibility between having proportional representation and having bicameralism. Federally, Australia has preferential voting (instant-runoff voting) in the House of Representatives and single transferrable vote is used to elect 12 senators for each state (only 6 in a normal election, the full 12 only get re-elected in a special "double dissolution" election, which the government is allowed to order to break a deadlock between the two houses). You mention Germany, which is a bicameral system as well (the Bundesrat).

For the benefits of federal bicameralism, consider the UK – England has almost 85% of the population, and so in a purely one-person-one-vote system will always outvote the other three constituent countries. The UK does have bicameralism, but non-federal – the House of Lords does not directly represent the constituent countries, and does not provide a mechanism to block an English majority – the majority of the House of Lords is English too. And I think this is one of the major factors driving the Scottish independence movement. If the UK had a system more like Australia – with an upper house providing equal representation to each part of the country, regardless of population, and with constitutional referendums requiring a double majority to pass (both a majority of the national population, and also a majority of the population in a majority of the states) – then I don't think the Scottish independence movement would have anywhere near as much steam as it has.