I believe most users split up these inventories and run them on different schedules.
We run the HW inventory daily - it is quick and painless and will give you updated Add/Remove Program data.
SW inventory gets run once a week using AeXRunControl for randomization.

True. It has much less impact for users, when these tasks are split up into pieces. The clients will take a short amount of time, for each task.

Thanks for the replies, I totally understand the need to split them up, but it looks like even if I do split them up it will still run the hardware inventory after the software inventory. Keep in mind that these are default .ini files.

figure out what your requirements are and create your own custom ini files to run whatever inventories you need.
Then create inventory tasks to run them whenever you want.
The first ini file would be used once a week or once a month (usually) to gather all inventory.  The 2nd ini file would be used on a daily schedule (for example) to gather only hw inventory minus the exclusions. 
To answer the question in your first post - there would be no reason to run an inventory with the 2nd ini right after running an inventory with the 1st ini.

There is less of a need for splitting up the inventories now, then when these schedules were defined, years ago. 

Also keep in mind the clean before run option on the full vs the delta inventory on the hardware and software.

One reason still exists for keeping the HW inventory split out and running on a more frequent schedule and that is if you are rolling out software fairly often and need to have regular checks to see which machines have received the software, the HW inventory takes less time to run than SW.  The OS Add Remove Programs table is a great way to check the status of a rollout that may involve deployment methods other than SW Delivery through NS.  This would of course depend on the dynamics of your environment.  If you would never need more frequency than weekly, then you could easily turn off the HW inventory task.