Rebasing a branch with merges

Here's the scenario:

I create a topic branch so one other developer and myself can work on a feature that takes 2 weeks to complete. During that 2 week period, changes are occurring on master that I need in my topic branch. Since I have a collaborator on the branch, I opt for merges instead of rebase.

Each day I merge from master to the topic branch, which changes code I'm actively working in and requires semantic changes (functions renamed, moved, etc).

Once I'm ready to merge the topic branch back into master, I have two options (bearing in mind the goal is to keep history as clean as possible. Furthermore this implies that the constant merging into topic from master has made the topic branch look unwieldy and difficult to audit):

1. Do a squash merge, which keeps history clean but we lose context
for the important bits (the commits representing units of work that
contribute to the topic itself).

2. Do a final rebase prior to merging.

#2 doesn't seem to be possible due to patch ordering. For example, if I have real commits after merge commits that depend on those changes from master being present as a base at that point in time, the rebase will cause the patch before it to no longer include those changes from master.

Is there a mechanism to rebase in this situation to both achieve a clean, linear history for the topic branch and allow fast forward merging if desired, while still not causing superfluous conflicts due to the merges being omitted during the rebase?

Thanks in advance for any advice in this scenario.